Microbial Community Structure in the Rhizosphere of Rice Plants

PubMed Central

Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

2016-01-01

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 rhizospheremore » 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.« less

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

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

PubMed Central

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

2014-01-01

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

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.

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

PubMed

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

2016-06-01

Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For

Engineering rhizosphere hydraulics: pathways to improve plant adaptation to drought

NASA Astrophysics Data System (ADS)

Ahmed, Mutez; Zarebanadkouki, Mohsen; Ahmadi, Katayoun; Kroener, Eva; Kostka, Stanley; Carminati, Andrea

2017-04-01

Developing new technologies to optimize the use of water in irrigated croplands is of increasing importance. Recent studies have drawn attention to the role of mucilage in shaping rhizosphere hydraulic properties and regulating root water uptake. During drying mucilage keeps the rhizosphere wet and conductive, but upon drying it turns hydrophobic limiting root water uptake. Here we introduced the concept of rhizoligands, defined as additives that 1) rewet the rhizosphere and 2) reduce mucilage swelling hereby reducing the rhizosphere conductivity. We then tested its effect on rhizosphere water dynamics and transpiration. The following experiments were carried out to test if selected surfactants behave as a rhizoligand. We used neutron radiography to monitor water redistribution in the rhizosphere of lupine and maize irrigated with water and rhizoligand solution. In a parallel experiment, we tested the effect of rhizoligand on the transpiration rate of lupine and maize subjected to repeated drying and wetting cycles. We also measured the effect of rhizoligand on the maximum swelling of mucilage and the saturated hydraulic conductivity of soil mixed with various mucilage concentrations. The results were then simulated using a root water uptake model. Rhizoligand treatment quickly and uniformly rewetted the rhizosphere of maize and lupine. Interestingly, rhizoligand also reduced transpiration during drying/wetting cycles. Evaporation from the bare soil was of minor importance. Our hypothesis is that the reduction in transpiration was triggered by the interaction between rhizoligand and mucilage exuded by roots. This hypothesis is supported by the fact that rhizoligand reduced the maximum swelling of mucilage, increased its viscosity, and decreased the hydraulic conductivity of soil-mucilage mixtures. The reduced conductivity of the rhizosphere induced a moderate stress to the plants reducing transpiration. Simulation with a reduced hydraulic conductivity of the

Soil solution Zn and pH dynamics in non-rhizosphere soil and in the rhizosphere of Thlaspi caerulescens grown in a Zn/Cd-contaminated soil.

PubMed

Luo, Y M; Christie, P; Baker, A J

2000-07-01

Temporal changes in soil solution properties and metal speciation were studied in non-rhizosphere soil and in the rhizosphere of the hyperaccumulator Thlaspi caerulescens J. & C. Presl (population from Prayon, Belgium) grown in a Zn- and Cd-contaminated soil. This paper focuses on soil solution Zn and pH dynamics during phytoextraction. The concentration of Zn in both non-rhizosphere and rhizosphere soil solutions decreased from 23 mg/l at the beginning to 2 mg/l at the end of the experiment (84 days after transplanting of seedlings), mainly due to chemical sorption. There was no significant difference in overall Zn concentration between the planted and the unplanted soil solutions (P > 0.05). Soil solution pH decreased initially and then increased slightly in both planted and unplanted soil zones. From 60 to 84 days after transplanting, the pH of the rhizosphere soil solution was higher than that of non-rhizosphere soil solution (P<0.05). Zn uptake by the hyperaccumulator plants was 8.8 mg per pot (each containing 1 kg oven-dry soil) on average. The data indicate that the potential of T. caerulescens to remove Zn from contaminated soil may not be related to acidification of the rhizosphere.

From data to knowledge: The future of multi-omics data analysis for the rhizosphere

DOE PAGES

Allen White III, Richard; Borkum, Mark I.; Rivas-Ubach, Albert; ...

2017-05-04

The rhizosphere is the interface between the root system of a plant and its surrounding soil. The microbiome of the rhizosphere, which is the totality of all microbes present there, represents a complex microbial ecosystem that nourishes the terrestrial biosphere. In order to untangle the complexity of the rhizosphere, and of the rhizospheric microbiome in particular, an integrated multi-omics approach can be applied to reveal the composition of the rhizospheric microbiome (through 16S ribosomal amplicons and metagenomics), the functional properties of the microbiome (through metatranscriptomics and metaproteomics), and the signaling network within the rhizosphere (through metametabolomics). The successful application ofmore » integrated multi-omics to rhizospheric science depends on the availability of rhizosphere-specific data and on the appropriate software used to analyze omics data from the rhizosphere. Here, we analyze the availability of software suites that are normally applied to surrogate disciplines (e.g., soil and plants) but which can be used for rhizospheric science. We also identify potential issues, challenges, and opportunities for rhizosphere science.« less

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

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. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

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

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

STRESS ETHYLENE: A BIOASSAY FOR RHIZOSPHERE-APPLIED PHYTOTOXICANTS

EPA Science Inventory

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

Diversity and heritability of the maize rhizosphere microbiome under field conditions

USDA-ARS?s Scientific Manuscript database

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

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. Copyright © 2016 The Authors. Published by Elsevier B.V. All

Rhizosphere Colonization and Control of Meloidogyne spp. by Nematode-trapping Fungi

PubMed Central

Persson, Christina; Jansson, Hans-Börje

1999-01-01

The ability of nematode-trapping fungi to colonize the rhizosphere of crop plants has been suggested to be an important factor in biological control of root-infecting nematodes. In this study, rhizosphere colonization was evaluated for 38 isolates of nematode-trapping fungi representing 11 species. In an initial screen, Arthrobotrys dactyloides, A. superba, and Monacrosporium ellipsosporum were most frequently detected in the tomato rhizosphere. In subsequent pot experiments these fungi and the non-root colonizing M. geophyropagum were introduced to soil in a sodium alginate matrix, and further tested both for establishment in the tomato rhizosphere and suppression of root-knot nematodes. The knob-forming M. ellipsosporum showed a high capacity to colonize the rhizosphere both in the initial screen and the pot experiments, with more than twice as many fungal propagules in the rhizosphere as in the root-free soil. However, neither this fungus nor the other nematode-trapping fungi tested reduced nematode damage to tomato plants. PMID:19270886

Plant-microbe interactions driven by exometabolite preferences of rhizosphere bacteria

NASA Astrophysics Data System (ADS)

Zhalnina, K.; Louie, K. B.; Mansoori, N.; Hao, Z.; Gao, J.; Cho, H. J.; Karaoz, U.; Loqué, D.; Bowen, B.; Firestone, M.; Brodie, E.; Northen, T.

2016-12-01

It is known that rhizosphere bacteria can impact important processes during plant development. In `return' plants release substantial quantities of soluble C into the soil surrounding its roots, attracting bacteria and other soil organisms. Given the potential beneficial and detrimental consequences of stimulating high densities of organisms adjacent to newly formed root, regulating the chemical composition of exudates would represent a potential means of plant selection for beneficial microorganisms. If exudate resource composition functions to select specific microorganisms, then one would expect that substrate specialization exists within the rhizosphere microbiome. Here we provide evidence that in the rhizosphere of wild oats (Avena barbata), specific metabolites are exuded that are preferentially used by selected bacteria in rhizosphere and this substrate specialization, together with the changing composition of root exudates, drives the observed successional patterns. To investigate the relationship between exudates and rhizosphere bacteria we first analyzed exudate composition of hydroponically grown plants using LC-MS/MS based metabolomics. We then designed a medium to simulate plant exudates and using this medium we examined the substrate preferences of a diversity of rhizosphere bacterial isolates. We then assessed the ability of soil isolates to consume exudate components by LC-MS/MS based metabolomics. These substrate preferences were then related to genomic features and successional patterns of bacteria in the Avena rhizosphere. The major fraction of plant exudates was found to be composed of amino- and carboxylic acids, sugars, nucleosides, quaternary amines and plant hormones. Amino acids, sugars and nucleosides were consumed by all analyzed isolates. However, isolates that were preferentially stimulated by plant growth, revealed substrate utilization preferences towards aromatic organic acids, while those not responding to growing roots did not

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

Bacterial diversity of Taxus rhizosphere: culture-independent and culture-dependent approaches.

PubMed

Hao, Da Cheng; Ge, Guang Bo; Yang, Ling

2008-07-01

The regional variability of Taxus rhizosphere bacterial community composition and diversity was studied by comparative analysis of three large 16S rRNA gene clone libraries from the Taxus rhizosphere in different regions of China (subtropical and temperate regions). One hundred and forty-six clones were screened for three libraries. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the abundance of sequences affiliated with Gammaproteobacteria, Betaproteobacteria, and Actinobacteria was higher in the library from the T. xmedia rhizosphere of the temperate region compared with the subtropical Taxus mairei rhizosphere. On the other hand, Acidobacteria was more abundant in libraries from the subtropical Taxus mairei rhizosphere. Richness estimates and diversity indices of three libraries revealed major differences, indicating a higher richness in the Taxus rhizosphere bacterial communities of the subtropical region and considerable variability in the bacterial community composition within this region. By enrichment culture, a novel Actinobacteria strain DICP16 was isolated from the T. xmedia rhizosphere of the temperate region and was identified as Leifsonia shinshuensis sp. via 16S rRNA gene and gyrase B sequence analyses. DICP16 was able to remove the xylosyl group from 7-xylosyl-10-deacetylbaccatin III and 7-xylosyl-10-deacetylpaclitaxel, thereby making the xylosyltaxanes available as sources of 10-deacetylbaccatin III and the anticancer drug paclitaxel. Taken together, the present studies provide, for the first time, the knowledge of the biodiversity of microorganisms populating Taxus rhizospheres.

[Transformation of Cu forms in Cynodon dactylon rhizosphere soil of copper tailings yard].

PubMed

Wang, You-bao; Huang, Yong-jie; Zhen, Quan; Yan, Mi; Yang, Hong-fei; Liu, Deng-yi

2007-06-01

The study on the Cu forms in Cynodon dactylon rhizosphere soil of copper tailings yard in Tongling City, Anhui Province showed that among the test Cu forms, the amount of residual form occupied the majority, while that of exchangeable form was relatively low. Compared with non-rhizosphere soil, rhizosphere soil had a higher organic matter content but a lower pH. With the growth of C. dactylon, the contents of organically combined and exchangeable Cu in rhizosphere soil increased by 7.89% and 5%, respectively, while those of carbonate-combined and Fe-Mn oxides-combined Cu decreased. The growth of C. dactylon accelerated the transformation of Cu forms in rhizosphere soil, and decreased the rhizosphere soil Cu content through its absorption.

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

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

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 ...

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

Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics

PubMed Central

2011-01-01

Background The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere. Results Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere. Conclusions Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants. PMID:22018401

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence.

PubMed

Mapelli, Francesca; Marasco, Ramona; Fusi, Marco; Scaglia, Barbara; Tsiamis, George; Rolli, Eleonora; Fodelianakis, Stilianos; Bourtzis, Kostas; Ventura, Stefano; Tambone, Fulvia; Adani, Fabrizio; Borin, Sara; Daffonchio, Daniele

2018-05-01

In mature soils, plant species and soil type determine the selection of root microbiota. Which of these two factors drives rhizosphere selection in barren substrates of developing desert soils has, however, not yet been established. Chronosequences of glacier forelands provide ideal natural environments to identify primary rhizosphere selection factors along the changing edaphic conditions of a developing soil. Here, we analyze changes in bacterial diversity in bulk soils and rhizospheres of a pioneer plant across a High Arctic glacier chronosequence. We show that the developmental stage of soil strongly modulates rhizosphere community assembly, even though plant-induced selection buffers the effect of changing edaphic factors. Bulk and rhizosphere soils host distinct bacterial communities that differentially vary along the chronosequence. Cation exchange capacity, exchangeable potassium, and metabolite concentration in the soil account for the rhizosphere bacterial diversity. Although the soil fraction (bulk soil and rhizosphere) explains up to 17.2% of the variation in bacterial microbiota, the soil developmental stage explains up to 47.7% of this variation. In addition, the operational taxonomic unit (OTU) co-occurrence network of the rhizosphere, whose complexity increases along the chronosequence, is loosely structured in barren compared with mature soils, corroborating our hypothesis that soil development tunes the rhizosphere effect.

Elucidating rhizosphere processes by mass spectrometry - A review.

PubMed

Rugova, Ariana; Puschenreiter, Markus; Koellensperger, Gunda; Hann, Stephan

2017-03-01

The presented review discusses state-of-the-art mass spectrometric methods, which have been developed and applied for investigation of chemical processes in the soil-root interface, the so-called rhizosphere. Rhizosphere soil's physical and chemical characteristics are to a great extent influenced by a complex mixture of compounds released from plant roots, i.e. root exudates, which have a high impact on nutrient and trace element dynamics in the soil-root interface as well as on microbial activities or soil physico-chemical characteristics. Chemical characterization as well as accurate quantification of the compounds present in the rhizosphere is a major prerequisite for a better understanding of rhizosphere processes and requires the development and application of advanced sampling procedures in combination with highly selective and sensitive analytical techniques. During the last years, targeted and non-targeted mass spectrometry-based methods have emerged and their combination with specific separation methods for various elements and compounds of a wide polarity range have been successfully applied in several studies. With this review we critically discuss the work that has been conducted within the last decade in the context of rhizosphere research and elemental or molecular mass spectrometry emphasizing different separation techniques as GC, LC and CE. Moreover, selected applications such as metal detoxification or nutrient acquisition will be discussed regarding the mass spectrometric techniques applied in studies of root exudates in plant-bacteria interactions. Additionally, a more recent isotope probing technique as novel mass spectrometry based application is highlighted. Copyright © 2017 Elsevier B.V. All rights reserved.

Changes in the bacterial community of soybean rhizospheres during growth in the field.

PubMed

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.

Imaging Nutrient Distribution in the Rhizosphere Using FTIR Imaging

DOE PAGES

Victor, Tiffany; Delpratt, Natalie; Cseke, Sarah Beth; ...

2017-03-06

Symbiotic associations in the rhizosphere between plants and microorganisms lead to efficient changes in the distribution of nutrients that promote growth and development for each organism involved. Understanding these nutrient fluxes provides insight into the molecular dynamics involved in nutrient transport from one organism to the other. Here, to study such a nutrient flow, a new application of Fourier transform infrared imaging (FTIRI) was developed that entailed growing Populus tremulodes seedlings on a thin, nutrient-enriched Phytagel matrix that allows pixel to pixel measurement of the distribution of nutrients, in particular, nitrate, in the rhizosphere. The FTIR spectra collected from ammoniummore » nitrate in the matrix indicated the greatest changes in the spectra at 1340 cm -1 due to the asymmetric stretching vibrations of nitrate. For quantification of the nitrate concentration in the rhizosphere of experimental plants, a calibration curve was generated that gave the nitrate concentration at each pixel in the chemical image. These images of the poplar rhizosphere showed evidence for symbiotic sharing of nutrients between the plant and the fungi, Laccaria bicolor, where the nitrate concentration was five times higher near mycorrhizal roots than further out into the rhizosphere. This suggested that nitrates are acquired and transported from the media toward the plant root by the fungi. Similarly, the sucrose used in the growth media as a carbon source was depleted around the fungi, suggesting its uptake and consumption by the system. In conclusion, this study is the first of its kind to visualize and quantify the nutrient availability associated with mycorrhizal interactions, indicating that FTIRI has the ability to monitor nutrient changes with other microorganisms in the rhizosphere as a key step for understanding nutrient flow processes in more diverse biological systems.« less

Imaging Nutrient Distribution in the Rhizosphere Using FTIR Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Victor, Tiffany; Delpratt, Natalie; Cseke, Sarah Beth

Symbiotic associations in the rhizosphere between plants and microorganisms lead to efficient changes in the distribution of nutrients that promote growth and development for each organism involved. Understanding these nutrient fluxes provides insight into the molecular dynamics involved in nutrient transport from one organism to the other. Here, to study such a nutrient flow, a new application of Fourier transform infrared imaging (FTIRI) was developed that entailed growing Populus tremulodes seedlings on a thin, nutrient-enriched Phytagel matrix that allows pixel to pixel measurement of the distribution of nutrients, in particular, nitrate, in the rhizosphere. The FTIR spectra collected from ammoniummore » nitrate in the matrix indicated the greatest changes in the spectra at 1340 cm -1 due to the asymmetric stretching vibrations of nitrate. For quantification of the nitrate concentration in the rhizosphere of experimental plants, a calibration curve was generated that gave the nitrate concentration at each pixel in the chemical image. These images of the poplar rhizosphere showed evidence for symbiotic sharing of nutrients between the plant and the fungi, Laccaria bicolor, where the nitrate concentration was five times higher near mycorrhizal roots than further out into the rhizosphere. This suggested that nitrates are acquired and transported from the media toward the plant root by the fungi. Similarly, the sucrose used in the growth media as a carbon source was depleted around the fungi, suggesting its uptake and consumption by the system. In conclusion, this study is the first of its kind to visualize and quantify the nutrient availability associated with mycorrhizal interactions, indicating that FTIRI has the ability to monitor nutrient changes with other microorganisms in the rhizosphere as a key step for understanding nutrient flow processes in more diverse biological systems.« less

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

Mycorrhizal diversity in the rhizosphere of sugarcane and grass on different soil types

NASA Astrophysics Data System (ADS)

Ratri Cahyani, Vita; Rastikawati, Dewi; Yuniardi, Nestri; Syamsiyah, Jauhari; Suntoro

2017-11-01

Mycorrhiza has been known well as beneficial microbiota for supporting plant growth and production. Understanding of the variability and the consistency of the mycorrhizal diversity on various habitats is important for developing mycorrhizal utilization. Mycorrhizal diversity in the rhizosphere of sugarcane from 4 (four) soil types and the rhizosphere of grass from 3 (three) soil types were investigated in the present study. The results showed that Glomus indicated as a versatile genus because it was found as a common and dominant genus in the sugarcane rhizosphere on all of four soil types (Alfisol, Andisol, Inceptisol, Vertisol) and in the grass rhizosphere on all of three soil types (Ultisol, Oxisol, Histosol). In addition, Acaulospora was found as a common genus in grass rhizosphere. Statistical analysis indicated that P availability in the rhizosphere of sugarcane had a significantly negative correlation with mycorrhizal spore density, in which decreasing P availability significantly related with increasing spore density.

From data to knowledge: The future of multi-omics data analysis for the rhizosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen White, Richard; Borkum, Mark I.; Rivas-Ubach, Albert

The rhizosphere is the interface between a plant's roots and its surrounding soil. The rhizosphere microbiome, a complex microbial ecosystem, nourishes the terrestrial biosphere. Integrated multi-omics is a modern approach to systems biology that analyzes and interprets the datasets of multiple -omes of both individual organisms and multi-organism communities and consortia. The successful usage and application of integrated multi-omics to rhizospheric science is predicated upon the availability of rhizosphere-specific data, metadata and software. This review analyzes the availability of multi-omics data, metadata and software for rhizospheric science, identifying potential issues, challenges and opportunities.

Effect of nematodes on rhizosphere colonization by seed-applied bacteria.

PubMed

Knox, Oliver G G; Killham, Ken; Artz, Rebekka R E; Mullins, Chris; Wilson, Michael

2004-08-01

There is much interest in the use of seed-applied bacteria for biocontrol and biofertilization, and several commercial products are available. However, many attempts to use this strategy fail because the seed-applied bacteria do not colonize the rhizosphere. Mechanisms of rhizosphere colonization may involve active bacterial movement or passive transport by percolating water or plant roots. Transport by other soil biota is likely to occur, but this area has not been well studied. We hypothesized that interactions with soil nematodes may enhance colonization. To test this hypothesis, a series of microcosm experiments was carried out using two contrasting soils maintained under well-defined physical conditions where transport by mass water flow could not occur. Seed-applied Pseudomonas fluorescens SBW25 was capable of rhizosphere colonization at matric potentials of -10 and -40 kPa in soil without nematodes, but colonization levels were substantially increased by the presence of nematodes. Our results suggest that nematodes can have an important role in rhizosphere colonization by bacteria in soil.

Rhizosphere Protists Change Metabolite Profiles in Zea mays.

PubMed

Kuppardt, Anke; Fester, Thomas; Härtig, Claus; Chatzinotas, Antonis

2018-01-01

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth.

Rhizosphere Protists Change Metabolite Profiles in Zea mays

PubMed Central

Kuppardt, Anke; Fester, Thomas; Härtig, Claus; Chatzinotas, Antonis

2018-01-01

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth. PMID:29780370

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.

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.

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

Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

PubMed Central

Mahmood, Shahid; Ekblad, Alf; Alström, Sadhna; Högberg, Nils; Finlay, Roger

2017-01-01

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel

Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape.

PubMed

Gkarmiri, Konstantia; Mahmood, Shahid; Ekblad, Alf; Alström, Sadhna; Högberg, Nils; Finlay, Roger

2017-11-15

RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13 CO 2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia , Proteobacteria , Planctomycetes , Acidobacteria , Gemmatimonadetes , Actinobacteria , and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13 C- and 12 C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces , Rhizobium , and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas ( Kaistobacter ) were dominant in rhizosphere soil. " Candidatus Nitrososphaera" was enriched in 13 C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12 C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13 C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13 C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13 CO 2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil

Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes

PubMed Central

Elhady, Ahmed; Adss, Shimaa; Hallmann, Johannes; Heuer, Holger

2018-01-01

Plant-parasitic nematodes cause considerable damage to crop plants. The rhizosphere microbiome can affect invasion and reproductive success of plant-parasitic nematodes, thus affecting plant damage. In this study, we investigated how the transplanted rhizosphere microbiome from different crops affect plant-parasitic nematodes on soybean or tomato, and whether the plant’s own microbiome from the rhizosphere protects it better than the microbiome from fallow soil. Soybean plants growing in sterilized substrate were inoculated with the microbiome extracted from the rhizosphere of soybean, maize, or tomato. Controls were inoculated with extracts from bulk soil, or not inoculated. After the microbiome was established, the root lesion nematode Pratylenchus penetrans was added. Root invasion of P. penetrans was significantly reduced on soybean plants inoculated with the microbiome from maize or soybean compared to tomato or bulk soil, or the uninoculated control. In the analogous experiment with tomato plants inoculated with either P. penetrans or the root knot nematode Meloidogyne incognita, the rhizosphere microbiomes of maize and tomato reduced root invasion by P. penetrans and M. incognita compared to microbiomes from soybean or bulk soil. Reproduction of M. incognita on tomato followed the same trend, and it was best suppressed by the tomato rhizosphere microbiome. In split-root experiments with soybean and tomato plants, a systemic effect of the inoculated rhizosphere microbiomes on root invasion of P. penetrans was shown. Furthermore, some transplanted microbiomes slightly enhanced plant growth compared to uninoculated plants. The microbiomes from maize rhizosphere and bulk soil increased the fresh weights of roots and shoots of soybean plants, and microbiomes from soybean rhizosphere and bulk soil increased the fresh weights of roots and shoots of tomato plants. Nematode invasion did not affect plant growth in these short-term experiments. In conclusion, this

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

Three-dimensional visualization and quantification of water content in the rhizosphere.

PubMed

Moradi, Ahmad B; Carminati, Andrea; Vetterlein, Doris; Vontobel, Peter; Lehmann, Eberhard; Weller, Ulrich; Hopmans, Jan W; Vogel, Hans-Jörg; Oswald, Sascha E

2011-11-01

• Despite the importance of rhizosphere properties for water flow from soil to roots, there is limited quantitative information on the distribution of water in the rhizosphere of plants. • Here, we used neutron tomography to quantify and visualize the water content in the rhizosphere of the plant species chickpea (Cicer arietinum), white lupin (Lupinus albus), and maize (Zea mays) 12 d after planting. • We clearly observed increasing soil water contents (θ) towards the root surface for all three plant species, as opposed to the usual assumption of decreasing water content. This was true for tap roots and lateral roots of both upper and lower parts of the root system. Furthermore, water gradients around the lower part of the roots were smaller and extended further into bulk soil compared with the upper part, where the gradients in water content were steeper. • Incorporating the hydraulic conductivity and water retention parameters of the rhizosphere into our model, we could simulate the gradual changes of θ towards the root surface, in agreement with the observations. The modelling result suggests that roots in their rhizosphere may modify the hydraulic properties of soil in a way that improves uptake under dry conditions. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

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

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

Water management impacts on arsenic speciation and iron-reducing bacteria in contrasting rice-rhizosphere compartments.

PubMed

Somenahally, Anil C; Hollister, Emily B; Yan, Wengui; Gentry, Terry J; Loeppert, Richard H

2011-10-01

Rice cultivated on arsenic (As) contaminated-soils will accumulate variable grain-As concentrations, as impacted by varietal differences, soil variables, and crop management. A field-scale experiment was conducted to study the impact of intermittent and continuous flooding on As speciation and microbial populations in rice rhizosphere compartments of soils that were either historically amended with As pesticide or unamended with As. Rhizosphere-soil, root-plaque, pore-water and grain As were quantified and speciated, and microbial populations in rhizosphere soil and root-plaque were characterized. Total-As concentrations in rhizosphere and grain were significantly lower in intermittently flooded compared to the continuously flooded plots (86% lower in pore-water, 55% lower in root-plaque and 41% lower in grain samples). iAs(V), iAs(III), and DMAs(V) were the predominant As species detected in rhizosphere-soil and root-plaque, pore-water and grain samples, respectively. Relative proportions of Archaea and iron-reducing bacteria (FeRB) were higher in rhizosphere soil compared to root-plaque. In rhizosphere soil, the relative abundance of FeRB was lower in intermittently flooded compared to continuously flooded plots, but there were no differences between root-plaque samples. This study has demonstrated that reductions in dissolved As concentrations in the rhizosphere and subsequent decreases in grain-As concentration can be attained through water management.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaplan, Daniel I.; Xu, Chen; Huang, Shan

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 weremore » 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« less

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

PubMed Central

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

2014-01-01

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

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity

PubMed Central

Bass, David; van der Gast, Christopher; Thomson, Serena; Neuhauser, Sigrid; Hilton, Sally; Bending, Gary D.

2018-01-01

Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence. PMID:29503632

Maximizing root/rhizosphere efficiency to improve crop productivity and nutrient use efficiency in intensive agriculture of China.

PubMed

Shen, Jianbo; Li, Chunjian; Mi, Guohua; Li, Long; Yuan, Lixing; Jiang, Rongfeng; Zhang, Fusuo

2013-03-01

Root and rhizosphere research has been conducted for many decades, but the underlying strategy of root/rhizosphere processes and management in intensive cropping systems remain largely to be determined. Improved grain production to meet the food demand of an increasing population has been highly dependent on chemical fertilizer input based on the traditionally assumed notion of 'high input, high output', which results in overuse of fertilizers but ignores the biological potential of roots or rhizosphere for efficient mobilization and acquisition of soil nutrients. Root exploration in soil nutrient resources and root-induced rhizosphere processes plays an important role in controlling nutrient transformation, efficient nutrient acquisition and use, and thus crop productivity. The efficiency of root/rhizosphere in terms of improved nutrient mobilization, acquisition, and use can be fully exploited by: (1) manipulating root growth (i.e. root development and size, root system architecture, and distribution); (2) regulating rhizosphere processes (i.e. rhizosphere acidification, organic anion and acid phosphatase exudation, localized application of nutrients, rhizosphere interactions, and use of efficient crop genotypes); and (3) optimizing root zone management to synchronize root growth and soil nutrient supply with demand of nutrients in cropping systems. Experiments have shown that root/rhizosphere management is an effective approach to increase both nutrient use efficiency and crop productivity for sustainable crop production. The objectives of this paper are to summarize the principles of root/rhizosphere management and provide an overview of some successful case studies on how to exploit the biological potential of root system and rhizosphere processes to improve crop productivity and nutrient use efficiency.

Increased acidification in the rhizosphere of cactus seedlings induced by Azospirillum brasilense

NASA Astrophysics Data System (ADS)

Carrillo, Angel; Li, Ching; Bashan, Yoav

2002-08-01

Acidification of the rhizosphere of cactus seedlings (giant cardon, Pachycereus pringlei) after inoculation with the plant growth-promoting bacterium Azospirillum brasilense Cd, in the presence or absence of ammonium and nitrate, was studied to understand how to increase growth of cardon seedlings in poor desert soils. While ammonium enhanced rhizosphere and liquid culture acidification, inoculation with the bacteria enhanced it further. On the other hand, nitrate increased pH of the rhizosphere, but combined with the bacterial inoculation, increase in pH was significantly smaller. Bacterial inoculation with ammonium enhanced plant growth.

Rates of root and organism growth, soil conditions, and temporal and spatial development of the rhizosphere.

PubMed

Watt, Michelle; Silk, Wendy K; Passioura, John B

2006-05-01

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. 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 (distance(2)/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. 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.

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

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China.

PubMed

Tang, Yulu; Zhong, Bifeng; Qu, Bing; Feng, Shujin; Ding, Sanglan; Su, Shijun; Li, Zhi; Gan, Zhiwei

2017-05-24

A total of 28 groundwater, paired farmland soil, lettuce, and its rhizosphere soil samples were collected from Chengdu, China to detect perchlorate levels and to evaluate the relationships of perchlorate concentrations among these matrices. The perchlorate concentrations in the groundwater, farmland soil, lettuce, and rhizosphere soil samples ranged from below detection limit to 60.2 μg L -1 , from below detection limit to 249 μg kg -1 dry weight (dw), from 2.07 to 1010 μg kg -1 wet weight, and from below detection limit to 314 μg kg -1 dw, respectively. Significant correlation was found in the perchlorate levels among the farmland soil, lettuce, and rhizosphere soil, suggesting that they have common pollution sources, or perchlorate might transfer from farmland soil-rhizosphere soil-plant. However, there is no significant correlation between groundwater and the other three matrices, indicating that infiltration from perchlorate contaminated farmland soil was not the predominant source for groundwater pollution in Chengdu. The perchlorate concentrations in the farmland soil and lettuce samples were significantly higher than those in the rhizosphere soil, primarily due to uptake of perchlorate through the rhizosphere micro-environment by lettuce, or accelerated degradation by rhizospheric microorganisms, which contributed more needs further investigation.

Root hairs increase root exudation and rhizosphere extension

NASA Astrophysics Data System (ADS)

Holz, Maire; Zarebandanadkouki, Mohsen; Kuzyakov, Yakov; Carmintati, Andrea

2017-04-01

Plant roots employ various mechanisms to increase their access to limited soil resources. An example of such strategies is the production of root hairs. Root hairs extend the root surface and therefore increase the access to nutrients. Additionally, carbon release from root hairs might facilitate nutrient uptake by spreading of carbon in the rhizosphere and enhancing microbial activity. The aim of this study was to test: i) how root hairs change the allocation of carbon in the soil-plant system; ii) whether root hairs exude carbon into the soil and iii) how differences in C release between plants with and without root hairs affect rhizosphere extension. We grew barley plants with and without root hairs (wild type: WT, bald root barley: brb) in rhizoboxes filled with a sandy soil. Root elongation was monitored over time. After 4 weeks of growth, plants were labelled with 14CO2. A filter paper was placed on the soil surface before labelling and was removed after 36 h. 14C imaging of the soil surface and of the filter paper was used to quantify the allocation of 14C into the roots and the exudation of 14C, respectively. Plants were sampled destructively one day after labeling to quantify 14C in the plant-soil system. 14CO2 release from soil over time (17 d) was quantified by trapping CO2 in NaOH with an additional subset of plants. WT and brb plants had a similar aboveground biomass and allocated similar amounts of 14C into shoots (170 KBq for WT; 152 KBq for brb) and roots one day after labelling. Biomass of root, rhizosphere soil as well as root elongation were lower for brb compared to the wild type. WT plants transported more C from the shoots to the roots (22.8% for WT; 13.8% for brb) and from the root into the rhizosphere (8.8% for WT 3.5% for brb). Yet lower amounts of 14CO2 were released from soil over time for WT. Radial and longitudinal rhizosphere extension was increased for WT compared to brb (4.7 vs. 2.6 mm; 5.6 vs. 3.1 cm). The total exudation which was

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.

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.

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

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.

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.

Rhizosphere Processes Are Quantitatively Important Components of Terrestrial Biogeochemical Cycles: Data & Models

NASA Astrophysics Data System (ADS)

Finzi, A.

2016-12-01

The rhizosphere is a hot spot and hot moment for biogeochemical cycles. Microbial activity, extracellular enzyme activity and element cycles are greatly enhanced by root derived carbon inputs. As such the rhizosphere may be an important driver of ecosystem responses to global changes such as rising temperatures and atmospheric CO2 concentrations. Empirical research on the rhizosphere is extensive but extrapolation of rhizosphere processes to large spatial and temporal scales is largely uninterrogated. Using a combination of field studies, meta-analysis and numerical models we have found good reason to think that scaling is possible. In this talk I discuss the results of this research and focus on the results of a new modeling effort that explicitly links root distribution and architecture with a model of microbial physiology to assess the extent to which rhizosphere processes may affect ecosystem responses to global change. Results to date suggest that root inputs of C and possibly nutrients (ie, nitrogen) impact the fate of new C inputs to the soil (ie, accumulation or loss) in response to warming and enhanced productivity at elevated CO2. The model also provides qualitative guidance on incorporating the known effects of ectomycorrhizal fungi on decomposition and rates of soil C and N cycling.

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

Cucumber rhizosphere microbial community response to biocontrol agent Bacillus subtilis B068150

USDA-ARS?s Scientific Manuscript database

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...

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

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.

New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

DOE PAGES

Hess, Nancy J.; Pasa-Tolic, Ljiljana; Bailey, Vanessa L.; ...

2017-04-12

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Nancy J.; Paša-Tolić, Ljiljana; Bailey, Vanessa L.

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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

Comparison between fractionation and bioavailability of trace elements in rhizosphere and bulk soils.

PubMed

Wang, Zhongwen; Shan, Xiao-Quan; Zhang, Shuzhen

2002-03-01

Rhizosphere is a microbiosphere and has quite different chemical, physical and biological properties from bulk soils. A greenhouse experiment was performed to compare the difference of fractionation and bioavailability of trace elements Cr, Ni, Zn, Cu, Pb and Cd between rhizosphere soil and bulk soil. In the meantime, the influence of air-drying on the fractionation and bioavailability was also investigated by using wet soil sample as a control. Soils in a homemade rhizobox were divided into four zones: rhizosphere, near rhizosphere, near bulk soil and bulk soil zones, which was designated as S1, S2, S3 and S4. Elemental speciations were fractionated to water soluble, exchangeable and carbonate bound (B1), Fe-Mn oxide bound (B2), and organic and sulfide bound (B3) by a sequential extraction procedure. Speciation differences were observed for elements Cr, Ni, Zn, Cu, Pb and Cd between the rhizosphere and bulk soils, and between the air-dried and wet soils as well. The concentrations of all six heavy metals in fraction B1 followed the order of S2 > S3 > S1 > S4 and for B2, the order was S2 > S3 S4 > S1. For B3, the order was S1 > S3 S4 > S2, while for Cd the order was S2 > S3 approximately/= S4 > S1. The air-drying increased elemental concentration in fractions B1 and B2 by 20-50% and decreased in fraction B3 by about 20-100%. Correlation analysis also indicated that the bioavailability correlation coefficient of fraction B1 in rhizosphere wet soil to plants was better than that between either air-dried or nonrhizosphere soils. Therefore, application of rhizosphere wet soils should be recommended in the future study on the speciation analysis of trace elements in soils and bioavailability.

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

Biomimetic measurement of allelochemical dynamics in the rhizosphere.

PubMed

Weidenhamer, Jeffrey D

2005-02-01

Polydimethylsiloxane (PDMS) materials were used to quantify levels of the photosynthesis inhibitor sorgoleone in the undisturbed rhizosphere of sorghum plants. The materials used included stir bars coated with PDMS (stir bar sorptive extraction), technical grade optical fiber coated with a thin film of PDMS (matrix-solid phase microextraction), and PDMS tubing. PDMS tubing retained the most sorgoleone. As analyzed by high performance liquid chromatography, amounts of sorgoleone retained on the PDMS materials increased with time. Other materials tested (polyurethane foam plugs, C18 and Tenax disks, and resin capsules) proved less suitable, as they were subject to sometimes extensive penetration by fine root hairs. These results demonstrate the potential for PDMS-based materials to monitor the release of allelochemicals in the undisturbed rhizosphere of allelopathic plants. Unlike extraction procedures that recover all available compounds present in the soil, PDMS functions in a manner more analogous to plant roots in sorbing compounds from soil solution or root exudates. Information on chemical dynamics in the rhizosphere is crucial for evaluating specific hypotheses of allelopathic effects, understanding allelopathic mechanisms, and assessing the importance of allelopathic processes in plant communities.

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

Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.

PubMed

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

2011-09-01

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.

The development of the rhizosphere: simulation of root exudation for two contrasting exudates: citrate and mucilage

NASA Astrophysics Data System (ADS)

Sheng, Cheng; Bol, Roland; Vetterlein, Doris; Vanderborght, Jan; Schnepf, Andrea

2017-04-01

Different types of root exudates and their effect on soil/rhizosphere properties have received a lot of attention. Since their influence of rhizosphere properties and processes depends on their concentration in the soil, the assessment of the spatial-temporal exudate concentration distribution around roots is of key importance for understanding the functioning of the rhizosphere. Different root systems have different root architectures. Different types of root exudates diffuse in the rhizosphere with different diffusion coefficient. Both of them are responsible for the dynamics of exudate concentration distribution in the rhizosphere. Hence, simulations of root exudation involving four kinds of plant root systems (Vicia faba, Lupinus albus, Triticum aestivum and Zea mays) and two kinds of root exudates (citrate and mucilage) were conducted. We consider a simplified root architecture where each root is represented by a straight line. Assuming that root tips move at a constant velocity and that mucilage transport is linear, concentration distributions can be obtained from a convolution of the analytical solution of the transport equation in a stationary flow field for an instantaneous point source injection with the spatial-temporal distribution of the source strength. By coupling the analytical equation with a root growth model that delivers the spatial-temporal source term, we simulated exudate concentration distributions for citrate and mucilage with MATLAB. From the simulation results, we inferred the following information about the rhizosphere: (a) the dynamics of the root architecture development is the main effect of exudate distribution in the root zone; (b) a steady rhizosphere with constant width is more likely to develop for individual roots when the diffusion coefficient is small. The simulations suggest that rhizosphere development depends in the following way on the root and exudate properties: the dynamics of the root architecture result in various

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

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.

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

Impact of selection on maize root traits and rhizosphere interactions

NASA Astrophysics Data System (ADS)

Schmidt, J. E.; Gaudin, A. C. M.

2017-12-01

Effects of domestication and breeding on maize have been well-characterized aboveground, but impacts on root traits and rhizosphere processes remain unclear. Breeding in high-inorganic-input environments may have negatively affected the ability of modern maize to acquire nutrients through foraging and microbial interactions in marginal and/or organically managed soils. Twelve maize genotypes representing a selection gradient (teosintes, landraces, open-pollinated parents of modern elite germplasm, and modern hybrids released 1934-2015) were grown in three soils varying in intensity of long-term management (unfertilized, organic, conventional) in the greenhouse. Recruitment of rhizosphere microbial communities, nutrient acquisition, and plant productivity were affected by genotype-by-soil interactions. Maize genotypes exhibit significant variation in their ability to obtain nutrients from soils of different management history, indicating the potential for re-integration of beneficial root and rhizosphere traits to increase adaptation to low-input agroecosystems.

Screening of antagonistic bacteria isolated from Amorphophallus konjac rhizosphere soil

NASA Astrophysics Data System (ADS)

Lin, Tianxing; Gong, Mingfu; Guan, Qinlan; Huang, Ying; Qin, Fang

2018-04-01

Bacteria lived in Amorphaphallus konjac rhizosphere soil have the potential ability of antagonistic bacterial pathogen activity against to Erwinia carotovora subsp carotovora (Ecc). The paper was to study and analyze all strains of 18 bacteria isolated from A. konjac rhizosphere soil with strong antagonistic effect against to Ecc and to identify antagonistic bacteria with morphology, physiology and biochemistry characteristic. The antagonistic bacterial pathogen activity of different bacterial strains were significantly different. Five of 18 strains isolated from A. konjac rhizosphere soil, including AKSB03, AKSB05, AKSB08, AKSB13 and AKSB16 was screened with antagonistic wider more than 15 mm in first screening test. Strain AKSB08 and strain AKSB16 had a strong antagonism activity for Ecc with antagonistic wider more than 20 mm in second screening test. Strain AKSB08 and strain AKSB16 belonged to Bacillus with morphology, physiology and biochemistry characteristic.

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

USDA-ARS?s Scientific Manuscript database

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

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.

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

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

PubMed

Valverde, Angel; 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.

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.

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization

PubMed Central

Dawson, Wayne; Hör, Jens; Egert, Markus; van Kleunen, Mark; Pester, Michael

2017-01-01

Plant growth can be affected by soil bacteria. In turn, plants are known to influence soil bacteria through rhizodeposits and changes in abiotic conditions. We aimed to quantify the phylotype richness and relative abundance of rhizosphere bacteria that are actually influenced in a plant species-specific manner and to determine the role of the disproportionately large diversity of low-abundance bacteria belonging to the rare biosphere (<0.1 relative abundance) in this process. In addition, we aimed to determine whether plant phylogeny has an influence on the plant species-specific rhizosphere bacterial community. For this purpose, 19 herbaceous plant species from five different plant orders were grown in a common soil substrate. Bacterial communities in the initial soil substrate and the established rhizosphere soils were compared by 16S rRNA gene amplicon sequencing. Only a small number of bacterial operational taxonomic units (OTUs, 97% sequence identity) responded either positively (ca. 1%) or negatively (ca. 1%) to a specific plant species. On average, 91% of plant-specific positive response OTUs comprised bacteria belonging to the rare biosphere, highlighting that low-abundance populations are metabolically active in the rhizosphere. In addition, low-abundance OTUs were in terms of their summed relative abundance major drivers of the bacterial phyla composition across the rhizosphere of all tested plant species. However, no effect of plant phylogeny could be observed on the established rhizosphere bacterial communities, neither when considering differences in the overall established rhizosphere communities nor when considering plant species-specific responders only. Our study provides a quantitative assessment of the effect of plants on their rhizosphere bacteria across multiple plant orders. Plant species-specific effects on soil bacterial communities involved only 18–111 bacterial OTUs out of several 1000s; this minority may potentially impact plant growth

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function.

PubMed

Mendes, Lucas William; Raaijmakers, Jos M; de Hollander, Mattias; Mendes, Rodrigo; Tsai, Siu Mui

2018-01-01

The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.

The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard Allen; Rivas-Ubach, Albert; Borkum, Mark I.

Over the past century, the significance of the rhizosphere has been increasingly recognized by the scientific community. Furthermore, this complex biological system is comprised of vast interconnected networks of microbial organisms that interact directly with their plant hosts, including archaea, bacteria, fungi, picoeukaryotes, and viruses. The rhizosphere provides a nutritional base to the terrestrial biosphere, and is integral to plant growth, crop production, and ecosystem health. There is little mechanistic understanding of the rhizosphere, but, and that constitutes a critical knowledge gap. It inhibits our ability to predict and control the terrestrial ecosystem to achieve desirable outcomes, such as bioenergymore » production, crop yield maximization, and soil-based carbon sequestration. Multi-omics have the potential to significantly advance our knowledge of rhizospheric science. Our review covers multi-omic techniques and technologies; methods and protocols for specific rhizospheric science questions; and the challenges to be addressed during this century of rhizospheric science.« less

The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard Allen; Rivas-Ubach, Albert; Borkum, Mark I.

Over the past century, the significance of the rhizosphere as a complex, biological system, comprised of vast, interconnected networks of microbial organisms that interact directly with their plant hosts (e.g., archæa, bacteria, fungi, eukaryotes, and viruses) has been increasingly recognized by the scientific community. Providing a nutritional base to the terrestrial biosphere, the rhizosphere is integral to plant growth, crop production and ecosystem health. Lack of mechanistic understanding of the rhizosphere constitutes a critical knowledge gap, inhibiting our ability to predict and control the terrestrial ecosystem in order to achieve desirable outcomes (e.g., bioenergy production, crop yield maximization, and soilbasedmore » carbon sequestration). Application of multi-omics has the potential to significantly advance our knowledge of rhizospheric science. This review covers: cutting- and bleeding-edge, multi-omic techniques and technologies; methods and protocols for specific rhizospheric science questions; and, challenges to be addressed during this century of rhizospheric science.« less

The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

DOE PAGES

White, Richard Allen; Rivas-Ubach, Albert; Borkum, Mark I.; ...

2017-05-06

Over the past century, the significance of the rhizosphere has been increasingly recognized by the scientific community. Furthermore, this complex biological system is comprised of vast interconnected networks of microbial organisms that interact directly with their plant hosts, including archaea, bacteria, fungi, picoeukaryotes, and viruses. The rhizosphere provides a nutritional base to the terrestrial biosphere, and is integral to plant growth, crop production, and ecosystem health. There is little mechanistic understanding of the rhizosphere, but, and that constitutes a critical knowledge gap. It inhibits our ability to predict and control the terrestrial ecosystem to achieve desirable outcomes, such as bioenergymore » production, crop yield maximization, and soil-based carbon sequestration. Multi-omics have the potential to significantly advance our knowledge of rhizospheric science. Our review covers multi-omic techniques and technologies; methods and protocols for specific rhizospheric science questions; and the challenges to be addressed during this century of rhizospheric science.« less

Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical Arbor, Melastoma malabathricum L.

PubMed

Sato, Atsuya; Watanabe, Toshihiro; Unno, Yusuke; Purnomo, Erry; Osaki, Mitsuru; Shinano, Takuro

2009-01-01

The diversity of diazotrophic bacteria in the rhizosphere of Melastoma malabathricum L. was investigated by cloning-sequencing of the nifH gene directly amplified from DNA extracted from soil. Samples were obtained from the rhizosphere and bulk soil of M. malabathricum growing in three different soil types (acid sulfate, peat and sandy clay soils) located very close to each other in south Kalimantan, Indonesia. Six clone libraries were constructed, generated from bulk and rhizosphere soil samples, and 300 nifH clones were produced, then assembled into 29 operational taxonomic units (OTUs) based on percent identity values. Our results suggested that nifH gene diversity is mainly dependent on soil properties, and did not differ remarkably between the rhizosphere and bulk soil of M. malabathricum except in acid sulfate soil. In acid sulfate soil, as the Shannon diversity index was lower in rhizosphere than in bulk soil, it is suggested that particular bacterial species might accumulate in the rhizosphere.

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

PubMed

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

2016-04-01

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.

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

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

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

Phyto-bioconversion of hard coal in the Cynodon dactylon/coal rhizosphere.

PubMed

Igbinigie, Eric E; Mutambanengwe, Cecil C Z; Rose, Peter D

2010-03-01

Fundamental processes involved in the microbial degradation of coal and its derivatives have been well documented. A mutualistic interaction between plant roots and certain microorganisms to aid growth of plants such as Cynodon dactylon (Bermuda grass) on hard coal dumps has recently been suggested. In the present study coal bioconversion activity of nonmycorrhizal fungi was investigated in the C. dactylon/coal rhizosphere. Fungal growth on 2% Duff-agar, gutation formation on nitric acid treated coal and submerged culture activity in nitrogen-rich and -deficient broth formed part of the screening and selection of the fungi. The selected fungal isolates were confirmed to be found in pristine C. dactylon/coal rhizosphere. To simulate bioconversion, a fungal aliquot of this rhizosphere was used as inoculum for a Perfusate fixed bed bioreactor, packed with coal. The results demonstrate an enhanced coal bioconversion facilitated by low molecular weight organics and the bioconversion of coal may be initiated by an introduction of nitrogen moieties to the coal substrate. These findings suggest a phyto-bioconversion of hard coal involving plant and microbes occurring in the rhizosphere to promote the growth of C. dactylon. An understanding of this relationship can serve as a benchmark for coal dumps rehabilitation as well as for the industrial scale bioprocessing of hard coal.

The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing.

PubMed

Hao, Da-Cheng; Zhang, Cai-Rong; Xiao, Pei-Gen

2018-06-01

In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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. Copyright © 2015 Elsevier GmbH. All rights reserved.

Probing the rhizosphere to define mineral organic relationships

NASA Astrophysics Data System (ADS)

Schulz, M. S.; Dohnalkova, A.; Stonestrom, D. A.

2016-12-01

Soil organic matter (SOM) accumulation and stabilization over time is an important process as soils are a large carbon reservoir in which feedbacks under changing climates are unclear. The association of SOM with poorly crystalline or short-range-ordered secondary minerals has been shown to be important for carbon stabilization. Commonly used soil extraction techniques display correlations of SOM with secondary phases but do not show causation. The fate of root exudates in soils and processes controlling exudate associations with mineral phases are as yet structurally undefined. Sub-micron exploration of in-situ relations provides valuable information on SOM-mineral interactions. Soils of the Santa Cruz (California) marine terrace chronosequence are used to illustrate changes in deep (> 1 m) rhizosphere through time. Cracks and soil ped faces are sites of high root density and organic matter (biofilm or mucilage) deposition. We employ a variety of scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM) techniques for high resolution imaging and elemental analyses of deep rhizosphere and associated carbon mineral interactions. In these coastal prairie soils microscopy reveals secondary clay minerals associated with and possibly forming from organic-rich mucilage that occurs along the aforementioned rooting networks on fracture surfaces. We hypothesize that the production of secondary clays in the rhizosphere is an important mode of C incorporation into secondary minerals.

[Rhizosphere microbial impacts of alleviating faba bean Fusarium wilt with inoculating AM fungi].

PubMed

Dong, Yan; Dong, Kun; Yang, Zhi Xian; Tang, Li; Zheng, Yi

2016-12-01

Greenhouse pot trials were conducted to investigate the effects of arbuscular mycorrhizal fungus (Glomus mosseae, Glomus tortuosum, Glomus intraradices and Glomus etunicatum) inoculation on the seedling growth, occurance of Fusarium wilt, population of Fusarium oxysporum and rhizosphere microbial community functional diversity in faba bean rhizosphere soil. Results showed that after inoculation of G. mosseae, G. tortuosum, G. intraradices and G. etunicatum, the shoot and root fresh mass of faba bean seedlings increased significantly, the disease index of faba bean fusarium wilt decreased significantly by 94.0%, 60.0%, 64.0% and 94.0%, respectively, the amount of F. oxysporum of faba bean rhizosphere decreased significantly by 98.6%, 74.3%, 77.8% and 90.4%, respectively. The best inhibitory effects to Fusarium wilt were with G. mosseae and G. etunicatum treatments. Inoculation of G. mosseae, G. tortuosum and G. etunicatum significantly increased carbon sources utilization ability of carbohydrates, amino acids, carboxylic acids and phenolic acids, with the average well color development (AWCD) value being increased by 34.4%, 31.5% and 50.8% respectively, but such significant differences were not observed with inoculation of G. intraradice. Principal component analyses showed that inoculation of G. mosseae, G. tortuosum and G. etunicatum fungi changed the rhizospheric microbial community composition. Correlation analyses showed that the utilization of carbohydrates carbon sources (β-Methyl-D-glucoside, D-Galacturonic acid, D-Mannitol, N-Acetyl-D-Glucosamine, D-Cellobiose,) and carboxylic acids carbon sources (D-Galactonic acid-γ-Lactone) were significantly increased after inoculation of G. tortuosum, and the utilization of L-Arginine and 4-Hydroxy benzoic acid significantly increased after inoculation of G. mosseae and G. etunicatum. Carbohydrates, carboxylic acids were main carbon sources utilized by rhizosphere microbes after G. tortuosum and G. intraradices

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve.

PubMed

Fonseca, Jose Pedro; Hoffmann, Luisa; Cabral, Bianca Catarina Azeredo; Dias, Victor Hugo Giordano; Miranda, Marcio Rodrigues; de Azevedo Martins, Allan Cezar; Boschiero, Clarissa; Bastos, Wanderley Rodrigues; Silva, Rosane

2018-02-05

Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon

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. Copyright © 2016. Published by Elsevier B.V.

[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.

Application of Struvite Alters the Antibiotic Resistome in Soil, Rhizosphere, and Phyllosphere.

PubMed

Chen, Qing-Lin; An, Xin-Li; Zhu, Yong-Guan; Su, Jian-Qiang; Gillings, Michael R; Ye, Zhi-Long; Cui, Li

2017-07-18

Struvite recovered from wastewater is a renewable source of phosphorus and nitrogen and can be used as fertilizer for plant growth. However, antibiotics and resistome can be enriched in the struvite derived from wastewater. Robust understanding of the potential risks after struvite application to soils has remained elusive. Here, we profiled antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in struvite, soil, rhizosphere and phyllosphere of Brassica using high-throughput quantitative PCR. A total of 165 ARGs and 10 MGEs were detected. Application of struvite was found to increase both the abundance and diversity of ARGs in soil, rhizosphere and phyllosphere. In addition, ARGs shared exclusively between Brassica phyllosphere and struvite were identified, indicating that struvite was an important source of ARGs found in phyllosphere. Furthermore, OTUs shared between rhizosphere and phyllosphere were found to significantly correlate with ARGs, suggesting that microbiota in leaf and root could interconnect and ARGs might transfer from struvite to the surface of plants via rhizosphere using bacteria as spreading medium. These findings demonstrated that struvite as an organic fertilizer can facilitate the spread of antibiotic resistance into human food chain and this environment-acquired antibiotic resistance should be put into human health risk assessment system.

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.

Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L.

PubMed

Jin, Hui; Yang, Xiao-Yan; Yan, Zhi-Qiang; Liu, Quan; Li, Xiu-Zhuang; Chen, Ji-Xiang; Zhang, Deng-Hong; Zeng, Li-Ming; Qin, Bo

2014-07-01

A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity. Copyright © 2014 Elsevier GmbH. All rights reserved.

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

Coupled Modeling of Rhizosphere and Reactive Transport Processes

NASA Astrophysics Data System (ADS)

Roque-Malo, S.; Kumar, P.

2017-12-01

The rhizosphere, as a bio-diverse plant root-soil interface, hosts many hydrologic and biochemical processes, including nutrient cycling, hydraulic redistribution, and soil carbon dynamics among others. The biogeochemical function of root networks, including the facilitation of nutrient cycling through absorption and rhizodeposition, interaction with micro-organisms and fungi, contribution to biomass, etc., plays an important role in myriad Critical Zone processes. Despite this knowledge, the role of the rhizosphere on watershed-scale ecohydrologic functions in the Critical Zone has not been fully characterized, and specifically, the extensive capabilities of reactive transport models (RTMs) have not been applied to these hydrobiogeochemical dynamics. This study uniquely links rhizospheric processes with reactive transport modeling to couple soil biogeochemistry, biological processes, hydrologic flow, hydraulic redistribution, and vegetation dynamics. Key factors in the novel modeling approach are: (i) bi-directional effects of root-soil interaction, such as simultaneous root exudation and nutrient absorption; (ii) multi-state biomass fractions in soil (i.e. living, dormant, and dead biological and root materials); (iii) expression of three-dimensional fluxes to represent both vertical and lateral interconnected flows and processes; and (iv) the potential to include the influence of non-stationary external forcing and climatic factors. We anticipate that the resulting model will demonstrate the extensive effects of plant root dynamics on ecohydrologic functions at the watershed scale and will ultimately contribute to a better characterization of efflux from both agricultural and natural systems.

Bioaugmentation and rhizosphere-assisted biodegradation as strategies for optimization of the dissipation capacity of biobeds.

PubMed

Campos, M; Perruchon, C; Karas, P A; Karavasilis, D; Diez, M C; Karpouzas, D G

2017-02-01

Biobeds are on-farm biodepuration systems whose efficiency rely on their high pesticide biodegradation capacity. We evaluated two optimization strategies, bioaugmentation and/or rhizosphere-assisted biodegradation, to maximize the dissipation capacity of biobeds. Iprodione was used as a model pesticide. Its dissipation and metabolism was determined in a biobed packing material inoculated with an iprodione-degrading Arthrobacter strain C1 (bioaugmentation, treatments B+C1) and/or seeded with ryegrass (rhizosphere-assisted biodegradation, treatments B+P). The impact of those strategies on the activity and composition of the microbial community was determined. Bioaugmentation accelerated the dissipation of iprodione which was further enhanced in the bioaugmented, rhizosphere-assisted treatment (treatment B+P+C1, Half-life (DT 50 ) = 3.4 d), compared to the non-bioaugmented, non rhizosphere-assisted control (DT 50  = 9.5 d, treatment B). Bioaugmentation resulted in the earlier formation of intermediate formation of metabolites I (3,5-dichlorophenyl-carboxamide), II (3,5-dichlorophenylurea acetate) and 3,5-dichloroaniline (3,5-DCA). The latter was further dissipated by the indigenous microbial community. Acid phosphatase (AP) and β-glucosidase (GLU) were temporarily stimulated in rhizosphere-assisted treatments, whereas a stimulation of the fluorescein diacetate (FDA) hydrolytic activity in the bioaugmented treatments coincided with the hydrolysis of iprodione. q-PCR showed that changes in the abundance of alpha-proteobacteria and firmicutes was driven by the presence of rhizosphere while bioaugmentation had no significant effect. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Effect of grafting on rhizosphere soil environment and its relationship with disease resistance and yield of pepper.

PubMed

Duan, Xi; Bi, Huan Gai; Wei, You Ying; Li, Ting; Wang, Hong Tao; Ai, Xi Zhen

2016-11-18

We investigated the effect of grafting on the root rhizosphere soil microorganisms, physical properties, nutrient content, soil-borne disease and yield of pepper, using 'Weishi' (WS) and 'Buyeding' (BYD) as rootstocks, the cultivar pepper 'Xinfeng 2' (XF) as scion, and the own-root (XF/XF) pepper as the control. The results indicated that XF/WS and XF/BYD significantly increased the populations of fungi and actinomycetes and the percentage of actinomycetes. 60 days after transplanting, the activities of catalase (CAT) and peroxidase (POD) were much higher in root rhizosphere soil of grafted pepper. 90 days after transplanting, the activities of phosphatase, invertase, urease, and nitrate reductase (NR) were much higher in root rhizosphere soil of XF/WS. In addition, The XF/WS and XF/BYD also highly increased hydrocarbon compounds in soil extraction, slightly increased electric conductivity (EC) but lowered nitrogen, phosphorus and potassium contents in root rhizosphere soil. Higher pH in root rhizosphere soil was found in XF/WS but not in XF/BYD. These data indicated that grafting could optimize the rhizosphere soil environment of pepper and enhance the resistance of soil-borne diseases. The yields of XF/WS and XF/BYD were increased by 40.8% and 28.7%, respectively.

Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

PubMed

Pires, Ana C C; Cleary, Daniel F R; Almeida, Adelaide; Cunha, Angela; Dealtry, Simone; Mendonça-Hagler, Leda C S; Smalla, Kornelia; Gomes, Newton C M

2012-08-01

Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.

Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples

PubMed Central

Pires, Ana C. C.; Cleary, Daniel F. R.; Almeida, Adelaide; Cunha, Ângela; Dealtry, Simone; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

2012-01-01

Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages. PMID:22660713

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

USDA-ARS?s Scientific Manuscript database

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...

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere

PubMed Central

Matilla, Miguel A; Espinosa-Urgel, Manuel; Rodríguez-Herva, José J; Ramos, Juan L; Ramos-González, María Isabel

2007-01-01

Background Mutualistic interactions less well known than those between rhizobia and legumes are commonly found between plants and bacteria, frequently pseudomonads, which colonize roots and adjacent soil areas (the rhizosphere). Results A global analysis of Pseudomonas putida genes expressed during their interaction with maize roots revealed how a bacterial population adjusts its genetic program to this lifestyle. Differentially expressed genes were identified by comparing rhizosphere-colonizing populations with three distinct controls covering a variety of nutrients, growth phases and life styles (planktonic and sessile). Ninety rhizosphere up-regulated (rup) genes, which were induced relative to all three controls, were identified, whereas there was no repressed gene in common between the experiments. Genes involved in amino acid uptake and metabolism of aromatic compounds were preferentially expressed in the rhizosphere, which reflects the availability of particular nutrients in root exudates. The induction of efflux pumps and enzymes for glutathione metabolism indicates that adaptation to adverse conditions and stress (oxidative) response are crucial for bacterial life in this environment. The finding of a GGDEF/EAL domain response regulator among the induced genes suggests a role for the turnover of the secondary messenger c-diGMP in root colonization. Several mutants in rup genes showed reduced fitness in competitive root colonization. Conclusion Our results show the importance of two selective forces of different nature to colonize the rhizosphere: stress adaptation and availability of particular nutrients. We also identify new traits conferring bacterial survival in this niche and open a way to the characterization of specific signalling and regulatory processes governing the plant-Pseudomonas association. PMID:17784941

Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

PubMed

Zhao, Dayong; He, Xiaowei; Huang, Rui; Yan, Wenming; Yu, Zhongbo

2017-07-01

Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[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

Rhizosphere Competence and Biocontrol Effect of Pseudomonas sp. RU47 Independent from Plant Species and Soil Type at the Field Scale.

PubMed

Schreiter, Susanne; Babin, Doreen; Smalla, Kornelia; Grosch, Rita

2018-01-01

Biocontrol inoculants often show inconsistency in their efficacy at field scale and the reason for this remains often unclear. A high rhizosphere competence of inoculant strains is assumed to be a key factor for successful biocontrol effects as the biocontrol strain has to compete with the indigenous microbial community in the rhizosphere. It is known that many factors, among them plant species and soil type shape the rhizosphere microbial community composition. However, microbial community composition in the rhizosphere can also be influenced by the presence of a pathogen. We hypothesized that plant species, soil type, and a pathogen affect the rhizosphere competence of a biocontrol strain and its biocontrol effect against a soil-borne pathogen. To test the hypothesis, we used an experimental plot system with three soil types (diluvial sand, alluvial loam, loess loam) kept under similar agricultural management at the same field site for 12 years. We investigate the rhizosphere competence of Pseudomonas sp. RU47 in two plant species (potato and lettuce) and its biocontrol effect against Rhizoctonia diseases. The colonization density of a rifampicin resistant mutant of RU47 in the rhizosphere of both crops was evaluated by plate counts. Bacterial community compositions were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from total community DNA. The inoculant RU47 was able to colonize the rhizosphere of both model crops in a sufficient density and to reduce disease severity of black scurf on potato and bottom rot on lettuce in all three soils. DGGE indicated that RU47 affected the bacterial community composition stronger in the rhizosphere of lettuce than in the potato rhizosphere. In contrast, the effect of the pathogen Rhizoctonia solani on the bacterial community was much stronger in the rhizosphere of potato than in the lettuce rhizosphere. A significant effect of RU47 on the Pseudomonas -specific gac

Rhizosphere Competence and Biocontrol Effect of Pseudomonas sp. RU47 Independent from Plant Species and Soil Type at the Field Scale

PubMed Central

Schreiter, Susanne; Babin, Doreen; Smalla, Kornelia; Grosch, Rita

2018-01-01

Biocontrol inoculants often show inconsistency in their efficacy at field scale and the reason for this remains often unclear. A high rhizosphere competence of inoculant strains is assumed to be a key factor for successful biocontrol effects as the biocontrol strain has to compete with the indigenous microbial community in the rhizosphere. It is known that many factors, among them plant species and soil type shape the rhizosphere microbial community composition. However, microbial community composition in the rhizosphere can also be influenced by the presence of a pathogen. We hypothesized that plant species, soil type, and a pathogen affect the rhizosphere competence of a biocontrol strain and its biocontrol effect against a soil-borne pathogen. To test the hypothesis, we used an experimental plot system with three soil types (diluvial sand, alluvial loam, loess loam) kept under similar agricultural management at the same field site for 12 years. We investigate the rhizosphere competence of Pseudomonas sp. RU47 in two plant species (potato and lettuce) and its biocontrol effect against Rhizoctonia diseases. The colonization density of a rifampicin resistant mutant of RU47 in the rhizosphere of both crops was evaluated by plate counts. Bacterial community compositions were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from total community DNA. The inoculant RU47 was able to colonize the rhizosphere of both model crops in a sufficient density and to reduce disease severity of black scurf on potato and bottom rot on lettuce in all three soils. DGGE indicated that RU47 affected the bacterial community composition stronger in the rhizosphere of lettuce than in the potato rhizosphere. In contrast, the effect of the pathogen Rhizoctonia solani on the bacterial community was much stronger in the rhizosphere of potato than in the lettuce rhizosphere. A significant effect of RU47 on the Pseudomonas-specific gacA fingerprints

[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.

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.

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

Anaerobic ethylene glycol degradation by microorganisms in poplar and willow rhizospheres.

PubMed

Carnegie, D; Ramsay, J A

2009-07-01

Although aerobic degradation of ethylene glycol is well documented, only anaerobic biodegradation via methanogenesis or fermentation has been clearly shown. Enhanced ethylene glycol degradation has been demonstrated by microorganisms in the rhizosphere of shallow-rooted plants such as alfalfa and grasses where conditions may be aerobic, but has not been demonstrated in the deeper rhizosphere of poplar or willow trees where conditions are more likely to be anaerobic. This study evaluated ethylene glycol degradation under nitrate-, and sulphate-reducing conditions by microorganisms from the rhizosphere of poplar and willow trees planted in the path of a groundwater plume containing up to 1.9 mol l(-1) (120 g l(-1)) ethylene glycol and, the effect of fertilizer addition when nitrate or sulphate was provided as a terminal electron acceptor (TEA). Microorganisms in these rhizosphere soils degraded ethylene glycol using nitrate or sulphate as TEAs at close to the theoretical stoichiometric amounts required for mineralization. Although the added nitrate or sulphate was primarily used as TEA, TEAs naturally present in the soil or CO(2) produced from ethylene glycol degradation were also used, demonstrating multiple TEA usage. Anaerobic degradation produced acetaldehyde, less acetic acid, and more ethanol than under aerobic conditions. Although aerobic degradation rates were faster, close to 100% disappearance was eventually achieved anaerobically. Degradation rates under nitrate-reducing conditions were enhanced upon fertilizer addition to achieve rates similar to aerobic degradation with up to 19.3 mmol (1.20 g) of ethylene glycol degradation l(-1) day(-1) in poplar soils. This is the first study to demonstrate that microorganisms in the rhizosphere of deep rooted trees like willow and poplar can anaerobically degrade ethylene glycol. Since anaerobic biodegradation may significantly contribute to the phytoremediation of ethylene glycol in the deeper subsurface, the need

Effect of clonal integration on nitrogen cycling in rhizosphere of rhizomatous clonal plant, Phyllostachys bissetii, under heterogeneous light.

PubMed

Li, Yang; Chen, Jing-Song; Xue, Ge; Peng, Yuanying; Song, Hui-Xing

2018-07-01

Clonal integration plays an important role in clonal plant adapting to heterogeneous habitats. It was postulated that clonal integration could exhibit positive effects on nitrogen cycling in the rhizosphere of clonal plant subjected to heterogeneous light conditions. An in-situ experiment was conducted using clonal fragments of Phyllostachys bissetii with two successive ramets. Shading treatments were applied to offspring or mother ramets, respectively, whereas counterparts were treated to full sunlight. Rhizomes between two successive ramets were either severed or connected. Extracellular enzyme activities and nitrogen turnover were measured, as well as soil properties. Abundance of functional genes (archaeal or bacterial amoA, nifH) in the rhizosphere of shaded, offspring or mother ramets were determined using quantitative polymerase chain reaction. Carbon or nitrogen availabilities were significantly influenced by clonal integration in the rhizosphere of shaded ramets. Clonal integration significantly increased extracellular enzyme activities and abundance of functional genes in the rhizosphere of shaded ramets. When rhizomes were connected, higher nitrogen turnover (nitrogen mineralization or nitrification rates) was exhibited in the rhizosphere of shaded offspring ramets. However, nitrogen turnover was significantly decreased by clonal integration in the rhizosphere of shaded mother ramets. Path analysis indicated that nitrogen turnover in the rhizosphere of shaded, offspring or mother ramets were primarily driven by the response of soil microorganisms to dissolved organic carbon or nitrogen. This unique in-situ experiment provided insights into the mechanism of nutrient recycling mediated by clonal integration. It was suggested that effects of clonal integration on the rhizosphere microbial processes were dependent on direction of photosynthates transport in clonal plant subjected to heterogeneous light conditions. Copyright © 2018 Elsevier B.V. All rights

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. Copyright © 2017 Elsevier B.V. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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...

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture

PubMed Central

2018-01-01

Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study. PMID:29570619

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

PubMed

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

2016-09-01

The rhizosphere is known as the most active biogeochemical layer of the soil. Therefore, it could be a beneficial environment for biotic methane oxidation. The aim of this study was to document - by means of batch incubation tests - the kinetics of CH4 oxidation in rhizosphere soils that were previously exposed to methane. Soils from three pre-exposure to CH4 zones were sampled: the never-before pre-exposed (NEX), the moderately pre-exposed (MEX) and the very pre-exposed (VEX). For each pre-exposure zone, the rhizosphere of several plant species was collected, pre-incubated, placed in glass vials and submitted to CH4 concentrations varying from 0.5% to 10%. The time to the beginning of CH4 consumption and the CH4 oxidation rate were recorded. The results showed that the fastest CH4 consumption occurred for the very pre-exposed rhizosphere. Specifically, a statistically significant difference in CH4 oxidation half-life was found between the rhizosphere of the VEX vegetated with a mixture of different plants and the NEX vegetated with ryegrass. This difference was attributed to the combined effect of the preconditioning level and plant species as well as to the organic matter content. Regardless of the preconditioning level, the oxidation rate values obtained in this study were comparable to those reported in the reviewed literature for mature compost. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

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

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

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. However, 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, promotermore » 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.« less

[Rhizosphere effect of nutrients in different maize soils with different fertility levels].

PubMed

Wu, L; Zhang, S

2000-08-01

Maize plants and soil samples were collected from Jilin Province to study the nutrient dynamics in soil-maize plant rhizosphere and their relationship with plant uptake. The results showed that NH4(+)-N and NO3(-)-N were accumulated in rhizospheric soil, and mainly controlled by the application of chemical fertilizers. Soil available P was depleted in high fertility fields, especially in high seedling density, while accumulated in low fertility fields. Soil available K was accumulated in rhizospheric soil, and its accumulation rate was higher in high fertility than in low fertility fields. The nutrient absorption amount was N approximately K > P for maize plant shoots and roots, but was N > K > P for seeds. The contribution rate of chemical fertilizers to maize yield was only 1/5-1/3 in Jilin Province, and the rest was contributed by the application of organic manure, such as chicken feces or cow feces, and by the mineralization of soil organic matter.

Species-specific effects of polyploidisation and plant traits of Centaurea maculosa and Senecio inaequidens on rhizosphere microorganisms.

PubMed

Thébault, Aurélie; Frey, Beat; Mitchell, Edward A D; Buttler, Alexandre

2010-08-01

Invasive plant species represent a threat to terrestrial ecosystems, but their effects on the soil biota and the mechanisms involved are not yet well understood. Many invasive species have undergone polyploidisation, leading to the coexistence of various cytotypes in the native range, whereas, in most cases, only one cytotype is present in the introduced range. Since genetic variation within a species can modify soil rhizosphere communities, we studied the effects of different cytotypes and ranges (native diploid, native tetraploid and introduced tetraploid) of Centaurea maculosa and Senecio inaequidens on microbial biomass carbon, rhizosphere total DNA content and bacterial communities of a standard soil in relation to plant functional traits. There was no overall significant difference in microbial biomass between cytotypes. The variation of rhizosphere total DNA content and bacterial community structure according to cytotype was species specific. The rhizosphere DNA content of S. inaequidens decreased with polyploidisation in the native range but did not vary for C. maculosa. In contrast, the bacterial community structure of C. maculosa was affected by polyploidisation and its diversity increased, whereas there was no significant change for S. inaequidens. Traits of S. inaequidens were correlated to the rhizosphere biota. Bacterial diversity and total DNA content were positively correlated with resource allocation to belowground growth and late flowering, whereas microbial biomass carbon was negatively correlated to investment in reproduction. There were no correlations between traits of the cytotypes of C. maculosa and corresponding rhizosphere soil biota. This study shows that polyploidisation may affect rhizosphere bacterial community composition, but that effects vary among plant species. Such changes may contribute to the success of invasive polyploid genotypes in the introduced range.

Rhizospheric soil and root endogenous fungal diversity and composition in response to continuous Panax notoginseng cropping practices.

PubMed

Tan, Yong; Cui, Yinshan; Li, Haoyu; Kuang, Anxiu; Li, Xiaoran; Wei, Yunlin; Ji, Xiuling

2017-01-01

Rhizosphere and endophytic fungal communities are considered critically important for plant health and soil fertility. In response to continuous cropping, Panax notoginseng becomes vulnerable to attack by fungal pathogens. In the present study, culture-independent Illumina MiSeq was used to investigate the rhizospheric and root endophytic fungi in response to continuous Panax notoginseng cropping practices. The results demonstrated that fungal diversity is increased inside the roots and in rhizospheric. Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota were the dominant phyla detected during the continuous cropping of Panax notoginseng. The fungal diversity in the rhizospheric soil and roots of root-rot P. notoginseng plants are less than that of healthy plants in the same cultivating year, thus showing that root-rot disease also affects the community structure and diversity of rhizospheric and root endophytic fungi. Similarities in the major fungal components show that endophytic fungal communities are similar to rhizospheric soil fungal community based on a specialized subset of organisms. Canonical correspondence analysis on the fungal communities in root-rot rhizospheric from both healthy plants and rotation soils reveals that the soil pH and organic matter have the greatest impact upon the microbial community composition during continuous cropping, whereas soil nutrition status does not significantly affect the fungal community composition in response to continuous cropping practices. In addition, the results suggest that the unclassified genera Leotiomycetes, Cylindrocarpon, Fusarium and Mycocentrospora are shown as the potential pathogens which are responsible for the obstacles in continuous cropping of P. notoginseng. Further exploration of these potential pathogens might be useful for the biological control of continuous cropping of P. notoginseng. Copyright © 2016 Elsevier GmbH. All rights reserved.

Effects of Intercropping with Potato Onion on the Growth of Tomato and Rhizosphere Alkaline Phosphatase Genes Diversity

PubMed Central

Wu, Xia; Wu, Fengzhi; Zhou, Xingang; Fu, Xuepeng; Tao, Yue; Xu, Weihui; Pan, Kai; Liu, Shouwei

2016-01-01

Background and Aims: In China, excessive fertilization has resulted in phosphorus (P) accumulation in most greenhouse soils. Intercropping can improve the efficiency of nutrient utilization in crop production. In this study, pot experiments were performed to investigate the effects of intercropping with potato onion (Allium cepa L. var. aggregatum G. Don) on tomato (Solanum lycopersicum L.) seedlings growth and P uptake, the diversity of rhizosphere phosphobacteria and alkaline phosphatase (ALP) genes in phosphorus-rich soil. Methods: The experiment included three treatments, namely tomato monoculture (TM), potato onion monoculture (OM), and tomato/potato onion intercropping (TI-tomato intercropping and OI-potato onion intercropping). The growth and P uptake of tomato and potato onion seedlings were evaluated. The dilution plating method was used to determine the population of phosphate-solubilizing bacteria (PSB) and phosphate-mineralizing bacteria (PMB). The genomic DNAs of PSB and PMB in the rhizosphere of tomato and potato onions were extracted and purified, and then, with the primer set of 338f /518r, the PCR amplification of partial bacterial 16S rDNA sequence was performed and sequenced to determine the diversities of PSB and PMB. After extracting the total genomic DNAs from the rhizosphere, the copy numbers and diversities of ALP genes were investigated using real-time PCR and PCR-DGGE, respectively. Results: Intercropping with potato onion promoted the growth and P uptake of tomato seedlings, but inhibited those of potato onion. After 37 days of transplanting, compared to the rhizosphere of TM, the soil pH increased, while the electrolytic conductivity and Olsen P content decreased (p < 0.05) in the rhizosphere of TI. The populations and diversities of PSB, PMB, and ALP genes increased significantly in the rhizosphere of TI, compared to the rhizosphere of TM. Conclusion: The results indicated that intercropping with potato onion promoted the growth and P

Effects of Intercropping with Potato Onion on the Growth of Tomato and Rhizosphere Alkaline Phosphatase Genes Diversity.

PubMed

Wu, Xia; Wu, Fengzhi; Zhou, Xingang; Fu, Xuepeng; Tao, Yue; Xu, Weihui; Pan, Kai; Liu, Shouwei

2016-01-01

In China, excessive fertilization has resulted in phosphorus (P) accumulation in most greenhouse soils. Intercropping can improve the efficiency of nutrient utilization in crop production. In this study, pot experiments were performed to investigate the effects of intercropping with potato onion (Allium cepa L. var. aggregatum G. Don) on tomato (Solanum lycopersicum L.) seedlings growth and P uptake, the diversity of rhizosphere phosphobacteria and alkaline phosphatase (ALP) genes in phosphorus-rich soil. The experiment included three treatments, namely tomato monoculture (TM), potato onion monoculture (OM), and tomato/potato onion intercropping (TI-tomato intercropping and OI-potato onion intercropping). The growth and P uptake of tomato and potato onion seedlings were evaluated. The dilution plating method was used to determine the population of phosphate-solubilizing bacteria (PSB) and phosphate-mineralizing bacteria (PMB). The genomic DNAs of PSB and PMB in the rhizosphere of tomato and potato onions were extracted and purified, and then, with the primer set of 338f /518r, the PCR amplification of partial bacterial 16S rDNA sequence was performed and sequenced to determine the diversities of PSB and PMB. After extracting the total genomic DNAs from the rhizosphere, the copy numbers and diversities of ALP genes were investigated using real-time PCR and PCR-DGGE, respectively. Intercropping with potato onion promoted the growth and P uptake of tomato seedlings, but inhibited those of potato onion. After 37 days of transplanting, compared to the rhizosphere of TM, the soil pH increased, while the electrolytic conductivity and Olsen P content decreased (p < 0.05) in the rhizosphere of TI. The populations and diversities of PSB, PMB, and ALP genes increased significantly in the rhizosphere of TI, compared to the rhizosphere of TM. The results indicated that intercropping with potato onion promoted the growth and P uptake of tomato in phosphorus-rich soil and

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil.

PubMed

Jing, Da-Wei; Liu, Fang-Chun; Wang, Ming-You; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao; Dong, Yu-Feng

2017-01-01

This study aimed to determine the effects of root pruning on the physicochemical characteristics and microbial activities of poplar rhizosphere soil. The root systems of 5-year-old poplar (Populus×euramericana cv. 'Neva') trees were manually pruned at 6, 8, or 10 times diameter at breast height (DBH) from the trunk (severe, moderate, and light, respectively) along both inter-row sides. Moderate root pruning significantly increased the concentrations of amino acids, organic acids, and total sugars in the root exudates and decreased the pH of rhizosphere soil. This treatment also increased the contents of available nitrogen, phosphorus, potassium, and total organic carbon as well as high-, medium-, and low-activity organic carbon in rhizosphere soil. Moreover, moderate pruning increased the contents of microbial biomass carbon and nitrogen, and enhanced basal respiration, in addition to decreasing the metabolic quotients in rhizosphere soil by 8.9%, 5.0%, and 11.4% compared with control, light, and severe root pruning treatments, respectively. Moderate pruning increased the growth rates of DBH, tree height, and volume to the highest levels. Furthermore, these indices were not significantly different between the light root pruning and control groups, but varied significantly between severe and moderate root-pruning treatments. Thus, root pruning, depending on the distance from the trunk, significantly influences the physicochemical properties and microbial activities in poplar rhizosphere soil.

Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cobo-Díaz, Jose F.; Fernández-González, Antonio J.; Villadas, Pablo J.

Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak ( Quercus pyrenaica Willd.) rhizospheric soil for three different development stages along an altitudinal gradient: (a) a low altitude, non-optimal site for forest maintenance; (b) an intermediate altitude, optimal site for a forest; and (c) a high altitude, expansion site with isolated trees but without a real forest canopy. We observed that, at each altitude, the same microbial taxa appear both in the taxonomic analysis of the whole metagenome and inmore » the functional analysis of the methane, sulfur and nitrogen metabolisms. Although there were no major differences at the functional level, there were significant differences in the abundance of each taxon at the phylogenetic level between the rhizospheres of the forest (low and intermediate altitudes) and the expansion site. Proteobacteria and Actinobacteria were the most differentially abundant phyla in forest soils compared to the expansion site rhizosphere. Moreover, Verrucomicrobia, Bacteroidetes and Nitrospirae phyla were more highly represented in the non-forest rhizosphere. Our study suggests that rhizospheric microbial communities of the same tree species may be affected by development stage and forest canopy cover via changes in soil pH and the C/N ratio.« less

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil

PubMed Central

Jing, Da-Wei; Liu, Fang-Chun; Wang, Ming-You; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao; Dong, Yu-Feng

2017-01-01

This study aimed to determine the effects of root pruning on the physicochemical characteristics and microbial activities of poplar rhizosphere soil. The root systems of 5-year-old poplar (Populus×euramericana cv. ‘Neva’) trees were manually pruned at 6, 8, or 10 times diameter at breast height (DBH) from the trunk (severe, moderate, and light, respectively) along both inter-row sides. Moderate root pruning significantly increased the concentrations of amino acids, organic acids, and total sugars in the root exudates and decreased the pH of rhizosphere soil. This treatment also increased the contents of available nitrogen, phosphorus, potassium, and total organic carbon as well as high-, medium-, and low-activity organic carbon in rhizosphere soil. Moreover, moderate pruning increased the contents of microbial biomass carbon and nitrogen, and enhanced basal respiration, in addition to decreasing the metabolic quotients in rhizosphere soil by 8.9%, 5.0%, and 11.4% compared with control, light, and severe root pruning treatments, respectively. Moderate pruning increased the growth rates of DBH, tree height, and volume to the highest levels. Furthermore, these indices were not significantly different between the light root pruning and control groups, but varied significantly between severe and moderate root-pruning treatments. Thus, root pruning, depending on the distance from the trunk, significantly influences the physicochemical properties and microbial activities in poplar rhizosphere soil. PMID:29117215

[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.

Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains

DOE PAGES

Cobo-Díaz, Jose F.; Fernández-González, Antonio J.; Villadas, Pablo J.; ...

2017-10-12

Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak ( Quercus pyrenaica Willd.) rhizospheric soil for three different development stages along an altitudinal gradient: (a) a low altitude, non-optimal site for forest maintenance; (b) an intermediate altitude, optimal site for a forest; and (c) a high altitude, expansion site with isolated trees but without a real forest canopy. We observed that, at each altitude, the same microbial taxa appear both in the taxonomic analysis of the whole metagenome and inmore » the functional analysis of the methane, sulfur and nitrogen metabolisms. Although there were no major differences at the functional level, there were significant differences in the abundance of each taxon at the phylogenetic level between the rhizospheres of the forest (low and intermediate altitudes) and the expansion site. Proteobacteria and Actinobacteria were the most differentially abundant phyla in forest soils compared to the expansion site rhizosphere. Moreover, Verrucomicrobia, Bacteroidetes and Nitrospirae phyla were more highly represented in the non-forest rhizosphere. Our study suggests that rhizospheric microbial communities of the same tree species may be affected by development stage and forest canopy cover via changes in soil pH and the C/N ratio.« less

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.

IMPACT OF SOIL MANAGEMENT ON COTTON RHIZOSPHERE BACTERIA

USDA-ARS?s Scientific Manuscript database

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

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

Fractal Feature of Particle-Size Distribution in the Rhizospheres and Bulk Soils during Natural Recovery on the Loess Plateau, China

PubMed Central

Song, Zilin; Zhang, Chao; Liu, Guobin; Qu, Dong; Xue, Sha

2015-01-01

The application of fractal geometry to describe soil structure is an increasingly useful tool for better understanding the performance of soil systems. Only a few studies, however, have focused on the structure of rhizospheric zones, where energy flow and nutrient recycling most frequently occur. We used fractal dimensions to investigate the characteristics of particle-size distribution (PSD) in the rhizospheres and bulk soils of six croplands abandoned for 1, 5, 10, 15, 20, and 30 years on the Loess Plateau of China and evaluated the changes over successional time. The PSDs of the rhizospheres and the fractal dimensions between rhizosphere soil and bulk soils during the natural succession differed significantly due to the influence of plant roots. The rhizospheres had higher sand (0.05–1.00 mm) contents, lower silt (<0.002 mm) contents, and lower fractal dimensions than the bulk soils during the early and intermediate successional stages (1–15 years). The fractal dimensions of the rhizosphere soil and bulk soil ranged from 2.102 to 2.441 and from 2.214 to 2.459, respectively, during the 30-year restoration. Rhizospheric clay and silt contents and fractal dimension tended to be higher and sand content tended to be lower as abandonment age increased, but the bulk soils had the opposite trend. Linear regression analysis indicated that the fractal dimensions of both the rhizospheres and bulk soils were significantly linearly correlated with clay, sand, organic-carbon, and total-nitrogen contents, with R 2 ranging from 0.526 to 0.752 (P<0.001). In conclusion, PSD differed significantly between the rhizosphere soil and bulk soil. The fractal dimension was a sensitive and useful index for quantifying changes in the properties of the different soil zones. This study will greatly aid the application of the fractal method for describing soil structure and nutrient status and the understanding of the performance of rhizospheric zones during ecological restoration. PMID

Immobilization of Lead Migrating from Contaminated Soil in Rhizosphere Soil of Barley (Hordeum vulgare L.) and Hairy Vetch (Vicia villosa) Using Hydroxyapatite.

PubMed

Katoh, Masahiko; Risky, Elsya; Sato, Takeshi

2017-10-23

This study conducted plant growth tests using a rhizobox system to quantitatively determine the distance of immobilization lead migrating from contaminated soil into uncontaminated rhizosphere soil, and to assess the lead phases accumulated in rhizosphere soil by sequential extraction. Without the hydroxyapatite, exchangeable lead fractions increased as the rhizosphere soil got closer to the contaminated soil. Exchangeable lead fractions were higher even in the rhizosphere soil that shares a boundary with the root surface than in the soil before being planted. Thus, plant growth of hairy vetch was lower in the soil without the hydroxyapatite than in the soil with the hydroxyapatite. The presence of hydroxyapatite may immobilize the majority of lead migrating from contaminated soil into the rhizosphere soil within 1 mm from the contaminated soil. The dominant lead fraction in the rhizosphere soil with the hydroxyapatite was residual. Thus, plant growth was not suppressed and the lead concentration of the plant shoot remained at the background level. These results indicate that the presence of hydroxyapatite in the rhizosphere soil at 5% wt may immobilize most of the lead migrating into the rhizosphere soil within 1 mm from the contaminated soil, resulting in the prevention of lead migration toward the root surface.

Immobilization of Lead Migrating from Contaminated Soil in Rhizosphere Soil of Barley (Hordeum vulgare L.) and Hairy Vetch (Vicia villosa) Using Hydroxyapatite

PubMed Central

Risky, Elsya; Sato, Takeshi

2017-01-01

This study conducted plant growth tests using a rhizobox system to quantitatively determine the distance of immobilization lead migrating from contaminated soil into uncontaminated rhizosphere soil, and to assess the lead phases accumulated in rhizosphere soil by sequential extraction. Without the hydroxyapatite, exchangeable lead fractions increased as the rhizosphere soil got closer to the contaminated soil. Exchangeable lead fractions were higher even in the rhizosphere soil that shares a boundary with the root surface than in the soil before being planted. Thus, plant growth of hairy vetch was lower in the soil without the hydroxyapatite than in the soil with the hydroxyapatite. The presence of hydroxyapatite may immobilize the majority of lead migrating from contaminated soil into the rhizosphere soil within 1 mm from the contaminated soil. The dominant lead fraction in the rhizosphere soil with the hydroxyapatite was residual. Thus, plant growth was not suppressed and the lead concentration of the plant shoot remained at the background level. These results indicate that the presence of hydroxyapatite in the rhizosphere soil at 5% wt may immobilize most of the lead migrating into the rhizosphere soil within 1 mm from the contaminated soil, resulting in the prevention of lead migration toward the root surface. PMID:29065529

Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L.

PubMed

Zhou, Xue; Tian, Lei; Zhang, Jianfeng; Ma, Lina; Li, Xiujun; Tian, Chunjie

2017-12-01

Sea buckthorn (Hippophae rhamnoides L.) is a pioneer plant used for land reclamation and an appropriate material for studying the interactions of symbiotic microorganisms because of its nitrogen-fixing root nodules and mycorrhiza. We used high-throughput sequencing to reveal the diversities and community structures of rhizospheric fungi and their link with nitrogen-fixing Frankia harbored in sea buckthorn collected along an altitude gradient from the Qinghai Tibet Plateau to interior areas. We found that the fungal diversities and compositions varied between different sites. Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla. The distribution of sea buckthorn rhizospheric fungi was driven by both environmental factors and the geographic distance. Among all examined soil characteristics, altitude, AP, and pH were found to have significant (p < 0.05) effect on the rhizospheric fungal community. The rhizospheric fungal communities became more distinct as the distance increased. Moreover, co-inertia analysis identified significant co-structures between Frankia and AMF communities in the rhizosphere of sea buckthorn. We conclude that at the large scale, there are certain linkages between nitrogen-fixing bacteria and the AMF expressed in the distributional pattern. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

DOE PAGES

Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.; ...

2017-06-24

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures ( P = 0.031) were observed inmore » the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without

Isolation, Characterization, and Transfer of Cryptic Gene-Mobilizing Plasmids in the Wheat Rhizosphere

PubMed Central

van Elsas, Jan Dirk; McSpadden Gardener, Brian B.; Wolters, Anneke C.; Smit, Eric

1998-01-01

A set of self-transmissible plasmids with IncQ plasmid-mobilizing capacity was isolated by triparental exogenous isolation from the wheat rhizosphere with an Escherichia coli IncQ plasmid host and a Ralstonia eutropha recipient. Three plasmids of 38 to 45 kb, denoted pIPO1, pIPO2, and pIPO3, were selected for further study. No selectable traits (antibiotic or heavy-metal resistance) were identified in these plasmids. The plasmids were characterized by replicon typing via PCR and hybridization with replicon-specific probes and other hybridizations. pIPO1 and pIPO3 were similar to each other, whereas pIPO2 was different. None of these plasmids belonged to any known incompatibility group. pIPO2 was selected for further work, and a mini-Tn5-tet transposon was inserted to confer selectability. Plasmid pIPO2 had a broad IncQ plasmid mobilization and self-transfer range among the alpha, beta, and gamma subclasses of the Proteobacteria but did not show productive transfer to gram-positive bacteria. Plasmid pIPO2 mobilized IncQ plasmid pIE723 from Pseudomonas fluorescens to diverse indigenous proteobacteria in the rhizosphere of field-grown wheat. Transfer of pIE723 to indigenous bacteria was not observed in the absence of added pIPO2. A specific PCR primer system and a probe were developed for the detection of pIPO2-type plasmids in soil and rhizosphere. Analysis of soil DNA provided evidence for the presence of pIPO2 in inoculated wheat rhizosphere soil in the field study, as well as in the rhizosphere of uninoculated wheat plants growing in soil microcosms. The system failed to identify major reservoirs of pIPO2 in a variety of other soils. PMID:9501428

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures ( P = 0.031) were observed inmore » the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without

[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.

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.

[Changes of diversity and composition of fungal communities in rhizosphere of Panax ginseng].

PubMed

Dong, Lin-Lin; Niu, Wei-Hao; Wang, Rui; Xu, Jiang; Zhang, Lian-Juan; Zhang, Jun; Chen, Shi-Lin

2017-02-01

Continuous cropping obstacles resulted in the yield losses of Panax ginseng, and affected the development of ginseng industry. Soil fungal communities participated in the key ecological process, and their changes of diversity and composition were related to the continuous cropping obstacles. We analyzed the changes of fungal diversity and composition in the rhizosphere of ginseng using the high-throughput sequencing method, stated the effects of ginseng cultivation on the micro-ecology, and provided effective strategies for overcoming continuous cropping obstacles. Compared to those of the forest soils, the fungal diversity of ginseng rhizosphere soils was increased, and the increasing trends were declined with an increasing years of ginseng cultivation; the relative abundance of Sordariomycetes, Alatospora, Eurotiomycetes, Leotiomycetes, Saccharomycetes, Mucorales and Pezizomycetes were increased in the rhizosphere of ginseng. Pearson's correlation index indicated that soil chemical perporties affected the relative abundance of fungal communities. pH was significantly related to the relative abundance of Dothideomycetes and Alatospora; the content of available potassium was markedly associated with the relative abundance of Dothideomycetes, Alatospora and Mucorales; the content of total nitrogen was significant correlation with the relative abundance of Sordariomycetes and Mucorales. These results indicated that fertilization was one of pivotal factors affecting the rhizosphere micro-ecology of ginseng, and optimization of fertilization system was an effective method to overcome continuous cropping obstacles. Copyright© by the Chinese Pharmaceutical Association.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

The effects of pig manure application on the spread of tetracycline resistance in bulk and cucumber rhizosphere soils: a greenhouse experiment.

PubMed

Kang, Yijun; Hao, Yangyang; Xia, Dan; Shen, Min; Li, Qing; Hu, Jian

2017-07-01

It is important to understand the dynamics of tetracycline-resistant bacteria (TRB) and tetracycline resistance genes (TRGs) in bulk and rhizosphere soils for evaluating the spread of TRGs from pig manure to human. In this work, a greenhouse experiment was conducted to investigate the difference in abundance of TRB, tetracycline-resistant Escherichia coli (TRE), tetracycline-resistant Pseudomonas spp. (TRP), and TRGs between bulk and cucumber rhizosphere soils. The application of pig manure resulted in the long-term persistence of TRB, TRE, TRP, and TRGs in bulk soil and rhizosphere of cucumber for at least 65 days. Pig manure application dose was the major driving force in altering the abundances of TRB and TRE, whereas TRP was disturbed mainly by compartment (bulk soil or rhizosphere). Both TRE and the percentage of TRE in bulk and rhizosphere soils increased linearly with an increase in dose of pig manure. The exponential relationships between pig manure dose and TRP along with TRP percentage were also noted. There were significant differences in the relative abundances of TRGs between bulk and cucumber rhizosphere soils, suggesting the use of pig manure exerted a more lasting impact on the spread of TRGs in the rhizosphere than in the bulk soil.

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. Copyright © 2015 Miranda-Ríos et al.

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.

Influence of indian mustard (Brassica juncea) on rhizosphere soil solution chemistry in long-term contaminated soils: a rhizobox study.

PubMed

Kim, Kwon-Rae; Owens, Gary; Kwon, Soon-lk

2010-01-01

This study investigated the influence of Indian mustard (Brassica juncea) root exudation on soil solution properties (pH, dissolved organic carbon (DOC), metal solubility) in the rhizosphere using a rhizobox. Measurement was conducted following the cultivation of Indian mustard in the rhizobox filled four different types of heavy metal contaminated soils (two alkaline soils and two acidic soils). The growth of Indian mustard resulted in a significant increase (by 0.6 pH units) in rhizosphere soil solution pH of acidic soils and only a slight increase (< 0.1 pH units) in alkaline soils. Furthermore, the DOC concentration increased by 17-156 mg/L in the rhizosphere regardless of soil type and the extent of contamination, demonstrating the exudation of DOC from root. Ion chromatographic determination showed a marked increase in the total dissolved organic acids (OAs) in rhizosphere. While root exudates were observed in all soils, the amount of DOC and OAs in soil solution varied considerably amongst different soils, resulting in significant changes to soil solution metals in the rhizosphere. For example, the soil solution Cd, Cu, Pb, and Zn concentrations increased in the rhizosphere of alkaline soils compared to bulk soil following plant cultivation. In contrast, the soluble concentrations of Cd, Pb, and Zn in acidic soils decreased in rhizosphere soil when compared to bulk soils. Besides the influence of pH and DOC on metal solubility, the increase of heavy metal concentration having high stability constant such as Cu and Pb resulted in a release of Cd and Zn from solid phase to liquid phase.

Deciphering the rhizosphere by liquid extraction surface analysis mass spectrometry (LESA-MS)

NASA Astrophysics Data System (ADS)

Chu, R. K.; Tfaily, M. M.; Handakumbura, P. P.; Paša-Tolić, L.; Anderton, C.

2016-12-01

Interactions of plants with their soil microenvironment and surrounding microbes are of major scientific importance for reasons ranging from understanding global carbon and nitrogen cycling to developing advanced crops. Gaining spatial information of the biochemical interactions that occur within the rhizosphere and other subsurface terrestrial ecosystems is an area of growing interest. Accordingly, development of analytical tools to probe and map molecular interactions in situ, and without intrusive and extensive sample preparation, would provide unique insights into the processes governing plant growth, nitrogen fixation and the metabolic exchange between the root and rhizobia, for example. Here, we will discuss the development of an application using LESA-MS—liquid extraction surface analysis mass spectrometry—that is capable of spatially characterizing molecular rhizospheric interactions in their native state and in a label-free manner. In LESA-MS, microextractions of a sample's surface are performed robotically, and we can either address points of interest (e.g., determined visually) or an entire area can be profiled in a serial fashion. Extracted molecules are then ionized by nanoelectrospray ionization (nano-ESI) and analyzed using high resolution and mass accuracy mass spectrometry (Fourier transform ion cyclotron resonance, FTICR MS). Because this analysis can be performed under ambient conditions, we are able to characterize the chemical distributions within the rhizosphere of a living plant. Here, we use Sorghum bicolor grown in a two-dimensional rhizobox that contains Turface clay as a model system, and used methanol-water as the solvent to characterize molecular distributions across the rhizosphere.

Environment and geographic distance differ in relative importance for determining fungal community of rhizosphere and bulk soil.

PubMed

Zhang, Kaoping; Adams, Jonathan M; Shi, Yu; Yang, Teng; Sun, Ruibo; He, Dan; Ni, Yingying; Chu, Haiyan

2017-09-01

Rhizospheric fungi play major roles in both natural and agricultural ecosystems. However, little is known about the determinants of their diversity and biogeographic patterns. Here, we compared fungal communities in rhizosphere and bulk soils of wheat fields in the North China Plain. The rhizosphere had a lower fungal diversity (observed OTUs and Chao1) than bulk soil, and a distinct fungal community structure in rhizosphere compared with bulk soil. The relative importance of environmental factors and geographic distance for fungal distribution differed between rhizosphere and bulk soil. Environmental factors were the primary cause of variations in total fungal community and major fungal phyla in bulk soil. By contrast, fungal communities in soils loosely attached to roots were predictable from both environmental factors and influences of geographic distance. Communities in soils tightly attached to roots were mainly determined by geographic distance. Our results suggest that both contemporary environment processes (present-day abiotic and biotic environment characters) and historical processes (spatial isolation, dispersal limitation occurred in the past) dominate variations of fungal communities in wheat fields, but their relative importance of all these processes depends on the proximity of fungal community to the plant roots. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Community Composition and Abundance of Anammox Bacteria in Cattail Rhizosphere Sediments at Three Phenological Stages.

PubMed

Zhou, Xiaohong; Zhang, Jinping; Wen, Chunzi

2017-11-01

The distribution of anammox bacteria in rhizosphere sediments of cattail (Typha orientalis) at different phenological stages was investigated. Results showed that the number of 16S rRNA gene copies of the anammox bacteria was considerably higher in the rhizosphere sediment than in the nonrhizosphere sediment and control sediment. The abundances of the anammox bacteria exhibited striking temporal variations in the three different cattail phenological stages. In addition, the Chao1 and Shannon H indexes of the anammox bacteria in cattail rhizosphere sediments had evident spatial and temporal variations at different phenological stages. Four anammox genera (Brocadia, Kuenenia, Jettenia, and a new cluster) were detected and had proportions of 34.18, 45.57, 0.63, and 19.62%, respectively. The CCA analysis results indicated that Cu, TN, Pb, and Zn were pivotal factors that affect anammox bacteria composition. The PCoA analysis results indicated that the community structure at the rhizosphere and nonrhizosphere sediments collected on July was relatively specific and was different from sediments collected on other months, suggesting that cattail can influence the community structures of the anammox bacteria at the maturity stage.

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 CO 2 has important effects on the rhizosphere microenvironment by influencing plant growth. Here, we investigated the response of the R. pseudoacacia rhizosphere microenvironment to elevated CO 2 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 CO 2 relative to ambient CO 2 ; however, l-asparaginase activity decreased. Addionally, elevated CO 2 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 CO 2 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 CO 2 . In addition, elevated CO 2 significantly (p < 0.05) enhanced the removal ratio of Cd and Pb in rhizosphere soils. Overall, elevated CO 2 benefited the rhizosphere microenvironment of R. pseudoacacia seedlings under heavy metal stress, which suggests that increased atmospheric CO 2 concentrations could have positive effects on soil fertility and rhizosphere microenvironment under heavy metals. Copyright © 2016 Elsevier Ltd. All rights reserved.

[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.

Transient nature of rhizosphere carbon elucidated by supercritical freon-22 extraction and 13C NMR analysis

Treesearch

Filipe G. Sanchez; Maurice M. Bursey

2002-01-01

The region immediately adjacent to established roots of mature trees has been termed the "reoccurring rhizosphere" and it has been hypothesized that organic matter input from fine root turnover, root exudates and sloughing may result in a build up of the soil carbon in this region. The "reoccurring rhizosphere" for first-, second- and third-order...

Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat (Triticum turgidum L.)

PubMed Central

Iannucci, Anna; Fragasso, Mariagiovanna; Beleggia, Romina; Nigro, Franca; Papa, Roberto

2017-01-01

Domestication has induced major genetic changes in crop plants to satisfy human needs and as a consequence of adaptation to agroecosystems. This adaptation might have affected root exudate composition, which can influence the interactions in the rhizosphere. Here, using two different soil types (sand, soil), we provide an original example of the impact of domestication and crop evolution on root exudate composition through metabolite profiling of root exudates for a panel of 10 wheat genotypes that correspond to the key steps in domestication of tetraploid wheat (wild emmer, emmer, durum wheat). Our data show that soil type can dramatically affect the composition of root exudates in the rhizosphere. Moreover, the composition of the rhizosphere metabolites is associated with differences among the genotypes of the wheat domestication groups, as seen by the high heritability of some of the metabolites. Overall, we show that domestication and breeding have had major effects on root exudates in the rhizosphere, which suggests the adaptive nature of these changes. PMID:29326736

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaplan, Daniel I.; Kukkadapu, Ravi; Seaman, John C.

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 collectedmore » 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.« less

[Effects of nitrogen application rate on faba bean fusarium wilt and rhizospheric microbial metabolic functional diversity].

PubMed

Dong, Yan; Yang, Zhi-xian; Dong, Kun; Tang, Li; Zheng, Yi; Hu, Guo-bin

2013-04-01

A field plot experiment was conducted to study the effects of different nitrogen (N) application rates on the microbial functional diversity in faba bean rhizosphere and the relationships between the microbial functional diversity and the occurrence of faba bean fusarium wilt. Four nitrogen application rates were installed, i. e. , N0(0 kg hm-2 , N1 (56. 25 kg hm-2) , N2(112. 5 kg hm-2), and N3 (168.75 kg hm-2), and Biolog microbial analysis system was applied to study the damage of faba bean fusarium wilt and the rhizospheric microbial metabolic functional diversity. Applying N (N1 N2, and N3) decreased the disease index of faba bean fusarium wilt and the quantity of Fusarium oxysporum significantly, and increased the quantities of bacteria and actinomyces and the ratios of bacteria/fungi and actinomyces/fungi significantly, with the peak values of bacteria and actinomyces, bacteria/fungi, and actinomyces/fungi, and the lowest disease index and F. oxysporum density in N2. As compared with N0, applying N increased the AWCD value significantly, but the effects of different N application rates on the ability of rhizospheric microbes in utilizing six types of carbon sources had definite differences. Under the application of N, the utilization rates of carbohydrates, carboxylic acids, and amino acids by the rhizospheric microbes were higher. Principal component analysis demonstrated that applying N changed the rhizospheric microbial community composition obviously, and the carbohydrates, carboxylic acids, and amino acids were the sensitive carbon sources differentiating the changes of the microbial community induced by N application. Applying N inhibited the utilization of carbohydrates and carboxylic acids but improved the utilization of amino acids and phenolic acids by the rhizospheric microbes, which could be one of the main reasons of applying N being able to reduce the harm of faba bean fusarium wilt. It was suggested that rationally applying N could increase the

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weisenberger, A. G.; Bonito, G.; Lee, S.

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.more » 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).« less

Rhizospheric effects on the microbial community of e-waste-contaminated soils using phospholipid fatty acid and isoprenoid glycerol dialkyl glycerol tetraether analyses.

PubMed

Song, Mengke; Cheng, Zhineng; Luo, Chunling; Jiang, Longfei; Zhang, Dayi; Yin, Hua; Zhang, Gan

2018-04-01

We performed the study of rhizospheric effects on soil microbial community structure, including bacteria, fungi, actinomycete, and archaea, at an electronic waste (e-waste) recycling site by analyzing the phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether (GDGT) contents. By comparing PLFA and isoprenoid GDGT profiles of rhizospheric and surrounding bulk soils of 11 crop species, we observed distinct microbial community structures. The total PLFA concentration was significantly higher in rhizospheric soils than in non-rhizospheric soils, whereas no obvious difference was found in the total isoprenoid GDGT concentrations. The microbial community structure was also different, with higher ratios of fungal-to-bacterial PLFAs (F/B) and lower relative abundance of Gram-positive bacteria in rhizospheric soils. The extent of rhizospheric effects varied among plant species, and Colocasia esculenta L. had the greatest positive effects on the total microbial biomass. Dissolved organic carbon and pH were the main environmental factors affecting the microbial community represented by PLFAs, while the archaeal community was influenced by copper and zinc in all soils. These results offer a comprehensive view of rhizospheric effects on microbes in heavy metal and persistent organic pollutant co-contaminated soil, and provide fundamental knowledge regarding microbial ecology in e-waste-contaminated soils.

Effects of elevated O₃ on microbes in the rhizosphere of mycorrhizal snap bean with different O₃ sensitivity.

PubMed

Wang, Shuguang; Wang, Fei; Diao, Xiaojun; He, Liansheng

2014-02-01

Elevated ozone (O₃) generally affects microbial biomass and community structure in rhizosphere, but these effects are unclear in mycorrhizal plants because arbuscular mycorrhizal (AM) fungi often benefit microbial growth in the rhizosphere. Here, we investigate the effects of elevated O₃ on microbial biomass and community structure in the rhizosphere of mycorrhizal snap bean (Phaseolus vulgaris L.) with different O₃ sensitivity (R123: O₃-tolerant plant; S156: O₃-sensitive plant) based on the phospholipid fatty acids (PLFAs) method. Compared with ambient O₃, elevated O₃ significantly decreased mycorrhizal colonization rates in the 2 genotypes, especially in S156 plants. The wet masses of shoot and root were decreased by elevated O₃ in the 2 genotypes independent of AM inoculation, but they were higher in the mycorrhizal plant than in the nonmycorrhizal plant independent of O₃ concentration. Elevated O₃ significantly decreased the relative proportion of specific fungal PLFAs in the nonmycorrhizal plant, but this effect disappeared in the mycorrhizal plant. The relative proportions of specific PLFAs of other microbial groups (Gram-positive, Gram-negative, and actinomycete) in the rhizosphere and all specific PLFAs in the hyphosphere were not affected by elevated O₃ independent of AM inoculation. In the rhizosphere of the 2 genotypes, microbial community structure was changed by AM inoculation and elevated O₃ as well as by their interaction; in the hyphosphere, however, microbial community structure was changed by elevated O₃ only in R123 plants. It is concluded that AM inoculation can offset negative effect of elevated O₃ on fungal biomass but seems to enhance shift of microbial community structure in rhizosphere under elevated O₃.

[Allelopathy autotoxicity effects of aquatic extracts from rhizospheric soil on rooting and growth of stem cuttings in Pogostemon cablin].

PubMed

Tang, Kun; Li, Ming; Dong, Shan; Li, Yun-qi; Huang, Jie-wen; Li, Long-ming

2014-06-01

To study the allelopathy effects of aquatic extracts from rhizospheric soil on the rooting and growth of stem cutting in Pogostemon cablin, and to reveal its mechanism initially. The changes of rhizogenesis characteristics and physic-biochemical during cutting seedlings were observed when using different concentration of aquatic extracts from rhizospheric soil. Aquatic extracts from rhizospheric soil had significant inhibitory effects on rooting rate, root number, root length, root activity, growth rate of cutting with increasing concentrations of tissue extracts; The chlorophyll content of cutting seedlings were decreased, but content of MDA were increased, and activities of POD, PPO and IAAO in cutting seedlings were affected. Aquatic extracts from rhizospheric soil of Pogostemon cablin have varying degrees of inhibitory effects on the normal rooting and growth of stem cuttings.

CuO Nanoparticle Dissolution and Toxicity to Wheat ( Triticum aestivum) in Rhizosphere Soil.

PubMed

Gao, Xiaoyu; Avellan, Astrid; Laughton, Stephanie; Vaidya, Rucha; Rodrigues, Sónia M; Casman, Elizabeth A; Lowry, Gregory V

2018-03-06

It has been suggested, but not previously measured, that dissolution kinetics of soluble nanoparticles such as CuO nanoparticles (NPs) in soil affect their phytotoxicity. An added complexity is that such dissolution is also affected by the presence of plant roots. Here, we measured the rate of dissolution of CuO NPs in bulk soil, and in soil in which wheat plants ( Triticum aestivum) were grown under two soil NP dosing conditions: (a) freshly added CuO NPs (500 mg Cu/kg soil) and (b) CuO NPs aged for 28 d before planting. At the end of the plant growth period (14 d), available Cu was measured in three different soil compartments: bulk (not associated with roots), loosely attached to roots, and rhizosphere (soil firmly attached to roots). The labile Cu fraction increased from 17 mg/kg to 223 mg/kg in fresh treatments and from 283 mg/kg to 305 mg/kg in aged treatments over the growth period due to dissolution. Aging CuO NPs increased the toxicity to Triticum aestivum (reduction in root maximal length). The presence of roots in the soil had opposite and somewhat compensatory effects on NP dissolution, as measured in rhizosphere soil. pH increased 0.4 pH units for fresh NP treatments and 0.6 pH units for aged NPs. This lowered CuO NP dissolution in rhizosphere soil. Exudates from T. aestivum roots also increased soluble Cu in pore water. CaCl 2 extractable Cu concentrations increaed in rhizosphere soil compared to bulk soil, from 1.8 mg/kg to 6.2 mg/kg in fresh treatment and from 3.4 mg/kg to 5.4 mg/kg in aged treatments. Our study correlated CuO NP dissolution and the resulting Cu ion exposure profile to phytotoxicity, and showed that plant-induced changes in rhizosphere conditions should be considered when measuring the dissolution of CuO NPs near roots.

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere.

PubMed

Kalam, Sadaf; Das, Subha Narayan; Basu, Anirban; Podile, Appa Rao

2017-05-01

Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members. Three facultatively oligotrophic PGPR were identified through 16S rRNA gene sequencing as Sphingobacterium sp. (P3), Variovorax sp. (P4), and Roseomonas sp. (A2); the latter being a new report of PGPR. In presence of selected PGPR strains, the changes in population densities of Acidobacteria were monitored in metagenomic DNA extracted from bulk and rhizospheric soils of tomato and black gram using real time qPCR. A gradual increase in equivalent cell numbers of Acidobacteria members was observed over time along with a simultaneous increase in plant growth promotion by test PGPR. We report characterization of three effective PGPR strains and their effects on indigenous, underexplored difficult-to-culture phylum-Acidobacteria. We suggest that putative interactions between these two bacterial groups thriving in rhizospheric soils could be beneficial for plant growth. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unique Rhizosphere Micro-characteristics Facilitate Phytoextraction of Multiple Metals in Soil by the Hyperaccumulating Plant Sedum alfredii.

PubMed

Hou, Dandi; Wang, Kai; Liu, Ting; Wang, Haixin; Lin, Zhi; Qian, Jie; Lu, Lingli; Tian, Shengke

2017-05-16

Understanding the strategies that the roots of hyperaccumulating plants use to extract heavy metals from soils is important for optimizing phytoremediation. The rhizosphere characteristics of Sedum alfredii, a hyperaccumulator, were investigated 6 months after it had been planted in weathered field soils contaminated with 5.8 μg of Cd g -1 , 1985.1 μg of Zn g -1 , 667.5 μg of Pb g -1 , and 698.8 μg of Cu g -1 . In contrast with the non-hyperaccumulating ecotype (NHE), the hyperaccumulating ecotype (HE) of S. alfredii was more tolerant to the metals, and higher levels of Cd and Zn accumulated. The HE was characterized by a unique rhizosphere, including extensive root systems, a reduced soil pH, a higher metal bioavailability, and increased rhizomicrobial activity. The bioavailability of metals was significantly correlated with the HE's unique bacterial communities (P < 0.005). The HE harbored abundant Streptomyces (9.43%, family Streptomycetaceae), Kribbella (1.08%, family Nocardioidaceae), and an unclassified genus (1.09%, family Nocardioidaceae) in its rhizosphere, a composition that differed from that of the NHE. PICRUSt analysis predicted high relative abundances of imputed functional profiles in the HE rhizosphere related to membrane transport and amino acid metabolism. This study reveals the rhizosphere characteristics, particularly the unique bacterial rhizobiome of a hyperaccumulator, that might provide a new approach to facilitating heavy metal phytoextraction.

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

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.

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

PubMed

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

2016-02-23

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.

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

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.

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.

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.

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

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard.

PubMed

Novello, Giorgia; Gamalero, Elisa; Bona, Elisa; Boatti, Lara; Mignone, Flavio; Massa, Nadia; Cesaro, Patrizia; Lingua, Guido; Berta, Graziella

2017-01-01

Microorganisms associated with Vitis vinifera (grapevine) can affect its growth, health and grape quality. The aim of this study was to unravel the biodiversity of the bacterial rhizosphere microbiota of grapevine in an integrated pest management vineyard located in Piedmont, Italy. Comparison between the microbial community structure in the bulk and rhizosphere soil (variable: space) were performed. Moreover, the possible shifts of the bulk and rhizosphere soil microbiota according to two phenological stages such as flowering and early fruit development (variable: time) were characterized. The grapevine microbiota was identified using metagenomics and next-generation sequencing. Biodiversity was higher in the rhizosphere than in the bulk soil, independent of the phenological stage. Actinobacteria were the dominant class with frequencies ≥ 50% in all the soil samples, followed by Proteobacteria, Gemmatimonadetes, and Bacteroidetes. While Actinobacteria and Proteobacteria are well-known as being dominant in soil, this is the first time the presence of Gemmatimonadetes has been observed in vineyard soils. Gaiella was the dominant genus of Actinobacteria in all the samples. Finally, the microbiota associated with grapevine differed from the bulk soil microbiota and these variations were independent of the phenological stage of the plant.

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.

Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils.

PubMed

Navarro-Noya, Yendi E; Jan-Roblero, Janet; González-Chávez, Maria del Carmen; Hernández-Gama, Regina; Hernández-Rodríguez, César

2010-05-01

In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources.

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

PubMed

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

Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar

PubMed Central

Ji, Jun; Wu, Haiying; Meng, Fang; Zhang, Mingrong; Zheng, Xiaobo; Wu, Cunxiang; Zhang, Zhengguang

2014-01-01

Previous studies have shown that methionine from root exudates affects the rhizosphere bacterial population involved in soil nitrogen fixation. A transgenic line of Zigongdongdou soybean cultivar (ZD91) that expresses Arabidopsis cystathionine γ-synthase resulting in an increased methionine production was examined for its influence to the rhizosphere bacterial population. Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved. In total, 87,267 sequences (approximately 10,908 per sample) were analyzed. We found that Acidobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes, Gemmatimonadetes, Firmicutes, and Verrucomicrobia constitute the dominant taxonomic groups in either the ZD91 transgenic line or parental cultivar ZD, and that there was no statistically significant difference in the rhizosphere bacterial community structure between the two cultivars. PMID:25079947

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

Linking the response of bacterial populations to plant development through analysis of rhizosphere-competence traits of soil bacteria

NASA Astrophysics Data System (ADS)

Cho, H. J.; Karaoz, U.; Zhalnina, K.; Firestone, M. K.; Brodie, E.

2016-12-01

A growing plant root exudes changing combinations of compounds including root litter and other detritus throughout its developmental stages, providing a major source of organic C for rhizosphere bacteria. Clear patterns of microbial succession have been observed in the rhizosphere of a number of plants. These patterns of microbial succession are likely key to the processing of soil organic carbon and nutrient recycling. What is less well understood are the microbial traits, or combinations of traits, selected for during plant development. Are these traits or trait-combinations conserved, and is phylogeny a useful integrator of traits? Understanding the mechanisms underlying ecological succession would enable improved prediction of future rhizosphere states and consequences for C and nutrient cycles. In this study, we resolve the responses of rhizosphere bacteria at strain-level during plant (Avena fatua) developmental stages using both isolation and metagenomic approaches. Metagenome reads from bulk and rhizosphere soils were mapped to the genomes of thirty nine bacterial isolates numerically abundant ( 0.5% in relative abundance) and phylogenetically representative of these soils, and also to ninety six metagenome-derived genome bins. Analysis of temporal coverage patterns demonstrate that bacteria can be classified as positive and negative rhizosphere responders, with traits associated with root exudate utilization being important. Significant strain level diversity was observed and variance in the temporal coverage patterns further distinguished closely related strains of the same genera. For example, while a number of strains from the Bradyrhizobia, Mesorhizobia and Mycobacteria all increased in coverage with root growth, suggesting that recently acquired traits are selected for. Candidate traits distinguishing closely related strains included those related to xylose and other plant cell-wall derived sugar utilization, motility and aromatic organic acid

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

PubMed

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

2015-04-01

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. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

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

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

Characterization of rhizosphere fungi from selenium hyperaccumulator and nonhyperaccumulator plants along the eastern Rocky Mountain Front Range.

PubMed

Wangeline, Ami L; Valdez, J Rodolfo; Lindblom, Stormy Dawn; Bowling, Keri L; Reeves, F Brent; Pilon-Smits, Elizabeth A H

2011-07-01

Selenium-hyperaccumulator plants can store over 1% (dry mass) Se in their tissues, despite the toxicity of this element at high concentrations across eukaryotes. These levels of Se can have widespread effects on the plant's ecological partners, including herbivores and pathogens. Still other partners seem to have coevolved Se tolerance. This is the first known study addressing the rhizosphere mycoflora of Se hyperaccumulators and aims to evaluate the rhizospheric fungal diversity and Se tolerance to further the knowledge of how these organisms interact with their host plants and survive in these extreme habitats. Rhizosphere fungi were isolated from Se-hyperaccumulator and nonaccumulator plant species collected from five sites in Colorado and Wyoming; four seleniferous sites and one nonseleniferous site. 259 isolates were identified to genus or species and evaluated for Se tolerance. Among the 24 represented genera, 11 comprised 86% of the isolates. The majority of isolates from the seleniferous sites were unaffected by 10 mg·L(-1) Se, irrespective of host plant (hyperaccumulator vs. nonaccumulator), while rhizosphere fungi from a control, nonseleniferous site were highly sensitive to Se at 10 mg·L(-1) and as a group were significantly less (α = 0.05) tolerant than the isolates from the seleniferous sites. Even though Se is a commonly used antifungal agent, these results suggest that rhizosphere fungi from seleniferous habitats have widespread Se tolerance, likely an adaptive advantage in their Se-rich habitat.

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.

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils.

PubMed

Poli, Anna; Lazzari, Alexandra; Prigione, Valeria; Voyron, Samuele; Spadaro, Davide; Varese, Giovanna Cristina

2016-01-01

Rhizosphere and root-associated microbiota are crucial in determining plant health and in increasing productivity of agricultural crops. To date, research has mainly focused on the bacterial dimension of the microbiota. However, interest in the mycobiota is increasing, since fungi play a key role in soil ecosystems. We examined the effect of plant genotype, soil, and of Fusarium oxysporum f. sp. lycopersici (Fol) on the cultivable component of rhizosphere and root-associated mycobiota of tomato. Resistant and susceptible varieties were cultivated on two different soils (A and B), under glasshouse conditions. Isolated fungi were identified by morphological and molecular approaches. Differences were found between the rhizosphere and the roots, which in general displayed a lower number of species. The structure of the mycobiota was significantly affected by the soil type in the rhizosphere as well as by the plant genotype within the roots (NPERMANOVA, p < 0.05). The addition of Fol changed the community structure, particularly in soil A, where Penicillium spp. and Fusarium spp. were the dominant responding fungi. Overall, the results indicated that i) soil type and plant genotype affect the fungal communities; ii) plant roots select few species from the rhizosphere; and iii) the fungal community structure is influenced by Fol. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

[Effects of phosphorus sources on phosphorus fractions in rhizosphere soil of wild barley genotypes with high phosphorus utilization efficiency].

PubMed

Cai, Qiu-Yan; Zhang, Xi-Zhou; Li, Ting-Xuan; Chen, Guang-Deng

2014-11-01

High P-efficiency (IS-22-30, IS-22-25) and low P-efficiency (IS-07-07) wild barley cultivars were chosen to evaluate characteristics of phosphorus uptake and utilization, and properties of phosphorus fractions in rhizosphere and non-rhizosphere in a pot experiment with 0 (CK) and 30 mg P · kg(-1) supplied as only Pi (KH2PO4), only Po (phytate) or Pi + Po (KH2PO4+ phytate). The results showed that dry matter and phosphorus accumulation of wild barley in the different treatments was ranked as Pi > Pi + Po > Po > CK. In addition, dry matter yield and phosphorus uptake of wild barley with high P-efficiency exhibited significantly greater than that with low P-efficiency. The concentration of soil available phosphorus was significantly different after application of different phosphorus sources, which was presented as Pi > Pi + Po > Po. The concentration of soil available phosphorus in high P-efficiency wild barley was significantly higher than that of low P-efficiency in the rhizosphere soil. There was a deficit in rhizosphere available phosphorus of high P-efficiency wild barley, especially in Pi and Pi+Po treatments. The inorganic phosphorus fractions increased with the increasing Pi treatment, and the concentrations of inorganic phosphorus fractions in soil were sorted as follows: Ca10-P > O-P > Fe-P > Al-P > Ca2-P > Ca8-P. The contents of Ca2-P and Ca8-P for high P-efficiency wild barley showed deficits in rhizosphere soil under each phosphorus source treatment. In addition, enrichment of Al-P and Fe-P was observed in Pi treatment in rhizosphere soil. The concentrations of organic phosphorus fractions in soil were sorted as follows: moderate labile organic phosphorus > moderate resistant, resistant organic phosphorus > labile organic phosphorus. The labile and moderate labile organic phosphorus enriched in rhizosphere soil and the greatest enrichment appeared in Pi treatment. Furthermore, the concentrations of moderate resistant organic phosphorus and resistant

Which fraction of soil organic matter is more vulnerable to rhizosphere priming effect?

NASA Astrophysics Data System (ADS)

Zhu, B.; Cheng, W.

2016-12-01

Rhizosphere priming effect (RPE) is defined as the stimulation or suppression of soil organic matter (SOM) decomposition by living roots. It remains unclear which fraction of SOM is more vulnerable to rhizosphere priming. We conducted two experiments in continuous 13CO2 labeling growth chamber to compare the intensity of RPE for the active (or labile) vs. slow (or recalcitrant) SOM. A sandy loam (Alfisol) was incubated at 20oC and 80% water holding capacity for different periods, which created a gradient in the relative proportion of active vs. slow SOM in the remaining soils. We then grew sunflower (Helianthus annuus) and soybean (Glycine max) in these remaining soils for 50 days under the same environmental conditions to compare the RPE of these two plant species on the decomposition of soils that varied in the lability of SOM. In both experiments, as the incubation proceeded from 1 to 8 to 14 months (in experiment 1) and the soil changed from freshly-sampled soil to two-year-incubated soil (in experiment 2), the intensity of RPE increased significantly even after accounting for the changes in root biomass or root-derived CO2. This result suggests that the slow (or recalcitrant) fraction of SOM is likely more vulnerable to rhizosphere priming compared to the active (or labile) fraction of SOM. Although the underlying mechanisms of this finding await further investigation, our study clearly shows that the main component of SOM (slow or recalcitrant SOM, decadal turnover) is vulnerable to rhizosphere priming. Therefore, the RPE has the potential to substantially regulate both short-term and long-term soil carbon dynamics.

Characterization of phosphorus availability in response to radial oxygen losses in the rhizosphere of Vallisneria spiralis.

PubMed

Han, Chao; Ren, Jinghua; Wang, Zhaode; Yang, Shika; Ke, Fan; Xu, Di; Xie, Xianchuan

2018-06-01

The viewpoint that radial oxygen loss (ROL) of submerged macrophytes induces changes in redox conditions and the associated phosphorus (P) availability has been indirectly confirmed at larger spatial scales using conventional, destructive techniques. However, critical information about microniches has largely been overlooked due to the lack of satisfactory in situ mapping technologies. In this study, we deployed a recently developed hybrid sensor in the rhizosphere of Vallisneria spiralis (V. spiralis) during two vegetation periods to provide 2-D imaging of the spatiotemporal co-distribution of oxygen (O 2 ) and P from a fixed observation point. Overall, the images of O 2 and P showed a high degree of spatiotemporal heterogeneity throughout the rhizosphere at the sub-mm scale. A clear decrease in the P mobilization corresponded well to the steep O 2 enhancement within a 2-mm-thick zone around younger V. spiralis root, indicating a significant coupling relationship between ROL and P availability. Surprisingly, despite significant diurnal shifts in ROL along the older V. spiralis roots, P availability did not fluctuate in a substantial part of the rhizosphere throughout the day; however, ROL increased the P immobilization significantly by changing the redox gradients at the outer rhizosphere. This study clearly demonstrates how continuous ROL of V. spiralis can play a major role in regulating P availability within the rhizosphere. The premise behind this statement is the discovery of how this continuous ROL can lead to the formation of three distinctive redox landscapes in the rooting sediment (oxic, suboxic, or anaerobic layers). Copyright © 2018 Elsevier Ltd. All rights reserved.

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. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veličković, Dušan; Anderton, Christopher R.

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

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.

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

Effects of cadmium amendments on low-molecular-weight organic acid exudates in rhizosphere soils of tobacco and sunflower.

PubMed

Chiang, Po-Neng; Wang, Ming Kuang; Chiu, Chih Yu; Chou, Shu-Yen

2006-10-01

To recognize physiological response of plants to cadmium (Cd) toxicity in rhizosphere of plants, the pot experiments were employed to investigate how low-molecular-weight organic acids (LMWOAs) were exudated from tobacco and sunflower roots of Cd-amended soils. The aims of this study were to assess the effect of LMWOAs on uptake of Cd by tobacco and sunflower under pot experiments, thus comparing the ability of tobacco and sunflower for phytoremediation. Surface soils (0-20 cm) were collected from Taichung Experiment Station (TC) (silty loam). Cadmium chloride (CdCl(2)) was amended into TC soil, giving Cd concentrations of 1, 5, 10 mg kg(-1) soil. Soils with different concentrations of Cd were put into 12 cm (i.d.) pots for incubation, and then 2-week-old tobacco and sunflower seedlings were transplanted into the pots. Tobacco and sunflower were grown in greenhouse for 50 days, respectively. The rhizosphere and bulk soils, and fresh plant tissues were collected after harvest. The Cd concentrations in the plant and transfer factor values in the sunflower were higher than that in the tobacco. No LMWOAs were detected by gas chromatograph in bulk soils, and low amounts of LMWOAs were found in uncontaminated rhizosphere soils. Acetic, lactic, glycolic, malic, maleic, and succinic acids were found in the tobacco and sunflower rhizosphere soils. Concentrations of LMWOAs increased with increasing amendment of Cd concentrations in tobacco and sunflower rhizosphere soils. Correlation coefficient (r) of concentrations of Cd amendment versus LMWOAs exudates of tobacco and sunflower were 0.85 and 0.98, respectively. These results suggest that the different levels of LMWOAs present in the rhizosphere soil play an important role in the solubilization of Cd that bound with soil particle into soil solution and then uptake by plants.

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. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Visualizing Rhizosphere Soil Structure Around Living Roots

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2008-12-01

The rhizosphere, a thin layer of soil (0 to 2 mm) surrounding a living root, is an important interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 ìm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

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

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

PubMed

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata , Avicennia marina , and Ceriops tagal , was undertaken using high - throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Make the rhizosphere great again: microbes build walls in soil that roots pay for

NASA Astrophysics Data System (ADS)

Hallett, Paul; Naveed, Muhammad; Raffan, Annette; Bengough, Glyn; Feeney, Debbie; Brown, Lawrie; Georgy, Timothy; Cooper, Laura; Daly, Keith; Koebernick, Nicolai; Sinclair, Ian; Roose, Tiina

2017-04-01

Plant roots physically manipulate surrounding soil to ease penetration, provide anchorage, improve water and nutrient capture and enhance gaseous exchange, with knock-on impacts to habitats for microorganisms, soil stabilisation and sequestering of carbon. Root traits that alter soil physical properties include exudates, root hairs, the extent of soil drying and root architecture. We are exploring the extent that different root traits physically manipulate soils, drawing on near isogenic crop lines that differ in root hairs, architecture and exudation, and new physical approaches that quantify rhizosphere impacts. These approaches include hydromechanical testing that bridge soil physics, soil biology and materials science, small-scale measurements and non-invasive imaging to measure the rhizosphere directly. We use these data in image based models that describe retention and transport of water and nutrients in the rhizosphere. Micromechanics tests have found that barley root exudates initially disperse soil, followed by gelling after secondary decomposition of these exudates by microbes. Maize root exudates, on the other hand, caused a large amount of gelling of the soil, whereas this impact decreased with microbial decomposition. From our data on exudate viscosity, contact angle and surface tension, we have modelled the direct impact on water retention and transport in the rhizosphere, using 3D CT imaging with Synchrotron XRay CT with sufficient resolution to detect root hairs. From these images, pore structure changes were found to be affected by the presence of root hairs in barley. This could have implications to resource capture by plants, showing a secondary impact of root hairs beyond expanding the volume of soil that roots access.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

PubMed Central

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D.; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem. PMID:29093705

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.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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.

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

PubMed

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

2016-01-01

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

PREDICTIVE MODEL OF CONJUGATIVE PLASMID TRANSFER IN THE RHIZOSPHERE AND PHYLLOSPHERE

EPA Science Inventory

A computer simulation model was used to predict the dynamics of survival and conjugation of Pseudomonas cepacia (carrying the transmissible recombinant plasmid R388:Tn1721) with a nonrecombinant recipient strain in simple rhizosphere and phyllosphere microcosms. lasmid transfer r...

Quantitative imaging of rhizosphere pH and CO2 dynamics with planar optodes.

PubMed

Blossfeld, Stephan; Schreiber, Christina Maria; Liebsch, Gregor; Kuhn, Arnd Jürgen; Hinsinger, Philippe

2013-07-01

Live imaging methods have become extremely important for the exploration of biological processes. In particular, non-invasive measurement techniques are key to unravelling organism-environment interactions in close-to-natural set-ups, e.g. in the highly heterogeneous and difficult-to-probe environment of plant roots: the rhizosphere. pH and CO2 concentration are the main drivers of rhizosphere processes. Being able to monitor these parameters at high spatio-temporal resolution is of utmost importance for relevant interpretation of the underlying processes, especially in the complex environment of non-sterile plant-soil systems. This study introduces the application of easy-to-use planar optode systems in different set-ups to quantify plant root-soil interactions. pH- and recently developed CO2-sensors were applied to rhizobox systems to investigate roots with different functional traits, highlighting the potential of these tools. Continuous and highly resolved real-time measurements were made of the pH dynamics around Triticum turgidum durum (durum wheat) roots, Cicer arietinum (chickpea) roots and nodules, and CO2 dynamics in the rhizosphere of Viminaria juncea. Wheat root tips acidified slightly, while their root hair zone alkalized their rhizosphere by more than 1 pH unit and the effect of irrigation on soil pH could be visualized as well. Chickpea roots and nodules acidified the surrounding soil during N2 fixation and showed diurnal changes in acidification activity. A growing root of V. juncea exhibited a large zone of influence (mm) on soil CO2 content and therefore on its biogeochemical surrounding, all contributing to the extreme complexity of the root-soil interactions. This technique provides a unique tool for future root research applications and overcomes limitations of previous systems by creating quantitative maps without, for example, interpolation and time delays between single data points.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brigmon, R. L.; Stanhopc, A.; Franck, M. M.

2005-05-26

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

Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems

PubMed Central

Kazerooni, Elham A.; Maharachchikumbura, Sajeewa S. N.; Rethinasamy, Velazhahan; Al-Mahrouqi, Hamed; Al-Sadi, Abdullah M.

2017-01-01

This study examined fungal diversity and composition in conventional (CM) and desert farming (DE) systems in Oman. Fungal diversity in the rhizosphere of tomato was assessed using 454-pyrosequencing and culture-based techniques. Both techniques produced variable results in terms of fungal diversity, with 25% of the fungal classes shared between the two techniques. In addition, pyrosequencing recovered more taxa compared to direct plating. These findings could be attributed to the ability of pyrosequencing to recover taxa that cannot grow or are slow growing on culture media. Both techniques showed that fungal diversity in the conventional farm was comparable to that in the desert farm. However, the composition of fungal classes and taxa in the two farming systems were different. Pyrosequencing revealed that Microsporidetes and Dothideomycetes are the two most common fungal classes in CM and DE, respectively. However, the culture-based technique revealed that Eurotiomycetes was the most abundant class in both farming systems and some classes, such as Microsporidetes, were not detected by the culture-based technique. Although some plant pathogens (e.g., Pythium or Fusarium) were detected in the rhizosphere of tomato, the majority of fungal species in the rhizosphere of tomato were saprophytes. Our study shows that the cultivation system may have an impact on fungal diversity. The factors which affected fungal diversity in both farms are discussed. PMID:28824590

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.

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.

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology.

PubMed

Wood, Jennifer L; Tang, Caixian; Franks, Ashley E

2018-01-01

Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the assembly of soil-bacterial communities using Illumina 16S rRNA profiling and the predictive metagenomic-profiling program, PICRUSt. Using predictions based on CSR theory, we hypothesized that Cd and the presence of a rhizosphere would affect community assembly. We predicted that the additional resource availability in the rhizosphere would enrich for competitive life strategists, while the presence of Cd would select for stress-tolerators. Traits identified as competitive followed CSR predictions, discriminating between rhizosphere and bulk-soil communities whilst stress-tolerance traits increased with Cd dose, but only in bulk-soil communities. These findings suggest that a bacterium's competitive attributes are critical to its ability to occupy and proliferate in a Cd-contaminated rhizosphere. Ruderal traits, which relate to community re-colonization potential, were synergistically decreased by the presence of the rhizosphere and Cd dose. Taken together this microcosm study suggests that the CSR theory is broadly applicable to microbial communities. Further work toward developing a simplified and robust strategy for microbial CSR classification will provide an ecologically meaningful framework to interpret community-level changes across a range of biomes.

Bacterial interactions in the rhizosphere of seagrass communities in shallow coastal lagoons.

PubMed

Donnelly, A P; Herbert, R A

1998-12-01

Rooted phanerogam communities in the shallow intertidal and subtidal coastal zone represent productive and healthy ecosystems. Inorganic nutrients are assimilated into seagrass biomass. Much of the organic matter resulting from moribund seagrass is rapidly mineralized, principally by bacteria. The microbial community of the rhizosphere is also highly active due to the supply of organic matter released during photosynthesis. This active sediment community plays an important role through carbon, nitrogen and phosphorous cycling in maintaining the stability and productivity of seagrass meadows. Over the last two decades, however, seagrass meadows in European coastal areas have declined due to increasing pollution. As eutrophication advances a trasition occurs from rooted phanerogram dominated communities to planktonic algal blooms and/or cyanobacterial blooms. Such changes represent the decline of a stable, high biodiversity habitat to an unstable one dominated by a few species. These changes of community structure can occur rapidly once the internal nutrient and organic matter control cycles are exceeded. A field investigation was undertaken to establish the spatial distribution of bacterial populations of Zostera noltii colonized and uncolonized sediment in the Bassin d'Arcachon, France. Bacteria were enumerated using both plate count and MPN techniques for different functional groups as well as determining the total bacterial populations present. Nitrogen fixation, ammonification, sulphate reduction rates, as well as alkaline phosphatase activity were also determined. Colonization of the Z. noltii roots and rhizomes was studied by light and scanning electron microscopy. Results confirmed that higher bacterial populations were present in the rhizosphere of Z. noltii compared to uncolonized sediments. Furthermore, electron microscopy identified the rhizome as the main site of colonization for a diverse range of morphological groups of bacteria. Sulphate reducing

Nontarget effects of foliar fungicide application on the rhizosphere: diversity of nifH gene and nodulation in chickpea field

PubMed Central

Yang, C; Hamel, C; Vujanovic, V; Gan, Y

2012-01-01

Aims This study explores nontarget effects of fungicide application on field-grown chickpea. Methods and Results Molecular methods were used to test the effects of foliar application of fungicide on the diversity and distribution of nifH genes associated with two chickpea cultivars and their nodulation. Treatments were replicated four times in a split-plot design in the field, in 2008 and 2009. Chemical disease control did not change the richness of the nifH genes associated with chickpea, but selected different dominant nifH gene sequences in 2008, as revealed by correspondence analysis. Disease control strategies had no significant effect on disease severity or nifH gene distribution in 2009. Dry weather conditions rather than disease restricted plant growth that year, suggesting that reduced infection rather than the fungicide is the factor modifying the distribution of nifH gene in chickpea rhizosphere. Reduced nodule size and enhanced N2-fixation in protected plants indicate that disease control affects plant physiology, which may in turn influence rhizosphere bacteria. The genotypes of chickpea also affected the diversity of the nifH gene in the rhizosphere, illustrating the importance of plant selective effects on bacterial communities. Conclusions We conclude that the chemical disease control affects nodulation and the diversity of nifH gene in chickpea rhizosphere, by modifying host plant physiology. A direct effect of fungicide on the bacteria cannot be ruled out, however, as residual amounts of fungicide were found to accumulate in the rhizosphere soil of protected plants. Significance and Impact of the Study Systemic nontarget effect of phytoprotection on nifH gene diversity in chickpea rhizosphere is reported for the first time. This result suggests the possibility of manipulating associative biological nitrogen fixation in the field. PMID:22335393

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.

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.

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

PubMed

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

2011-04-01

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

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. Copyright © 2015 Elsevier B.V. All rights reserved.

Response of edible amaranth cultivar to salt stress led to Cd mobilization in rhizosphere soil: A metabolomic analysis.

PubMed

Guo, Shi-Hong; Hu, Ni; Li, Qu-Sheng; Yang, Ping; Wang, Li-Li; Xu, Zhi-Min; Chen, Hui-Jun; He, Bao-Yan; Zeng, Eddy Y

2018-05-31

The present study aimed to investigate the metabolic response of edible amaranth cultivars to salt stress and the induced rhizosphere effects on Cd mobilization in soil. Two edible amaranth cultivars (Amaranthus mangostanus L.), Quanhong (low-Cd accumulator; LC) and Liuye (high-Cd accumulator; HC), were subject to salinity treatment in both soil and hydroponic cultures. The total amount of mobilized Cd in rhizosphere soil under salinity treatment increased by 2.78-fold in LC cultivar and 4.36-fold in HC cultivar compared with controls, with 51.2% in LC cultivar and 80.5% in HC cultivar being attributed to biological mobilization of salinity. Multivariate statistical analysis generated from metabolite profiles in both rhizosphere soil and root revealed clear discrimination between control and salt treated samples. Tricarboxylic acid cycle in root was up-regulated to cope with salinity treatment, which promoted release of organic acids from root. The increased accumulation of organic acids in rhizosphere under salt stress obviously promoted soil Cd mobility. These results suggested that salinity promoted release of organic acids from root and enhanced soil Cd mobilization and accumulation in edible amaranth cultivar in soil culture. Copyright © 2018 Elsevier Ltd. All rights reserved.

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome.

PubMed

Zhang, Yunzeng; Xu, Jin; Riera, Nadia; Jin, Tao; Li, Jinyun; Wang, Nian

2017-08-10

Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease. In this study, we address this question using the citrus root-associated microbiome as a model. We identified the rhizosphere-to-rhizoplane-enriched taxonomic and functional properties of the citrus root-associated microbiome and determined how they were affected by Huanglongbing (HLB), a severe systemic disease caused by Candidatus Liberibacter asiaticus, using metagenomic and metatranscriptomic approaches. Multiple rhizoplane-enriched genera were identified, with Bradyrhizobium and Burkholderia being the most dominant. Plant-derived carbon sources are an important driving force for the enrichment process. The enrichment of functional attributes, such as motility, chemotaxis, secretion systems, and lipopolysaccharide (LPS) synthesis, demonstrated more active microbe-plant interactions on the rhizoplane than the rhizosphere. We observed that HLB impaired the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome in three ways: (1) by decreasing the relative abundance of most rhizoplane-enriched genera; (2) by reducing the relative abundance and/or expression activity of the functional attributes involved in microbe-plant interactions; and (3) by recruiting more functional features involved in autotrophic life cycle adaptation, such as carbon fixation and nitrogen nitrification in the HLB rhizoplane microbiome. Finally, our data showed that inoculation of Burkholderia strains isolated from the healthy citrus root

Root-feeding insects and their interactions with organisms in the rhizosphere.

PubMed

Johnson, Scott N; Rasmann, Sergio

2015-01-07

Root-feeding insects are an increasingly studied group of herbivores whose impacts on plant productivity and ecosystem processes are widely recognized. Their belowground habitat has hitherto hindered our understanding of how they interact with other organisms that share the rhizosphere. A surge in research in this area has now shed light on these interactions. We review key interactions between root-feeding insects and other rhizospheric organisms, including beneficial plant microbes (mycorrhizal fungi, nitrogen-fixing bacteria), antagonists/pathogens of root herbivores (arthropod predators, entomopathogenic nematodes/fungi, and bacterial pathogens), competitors, symbiotic microbes, and detritivores. Patterns for these interactions are emerging. The negative impacts of mycorrhizal fungi on root herbivores, for instance, raise the intriguing prospect that these fungi could be used for pest management. Moreover, a better understanding of symbiotic microbes in root herbivores, especially those underpinning digestion, could prove useful in industries such as biofuel production.

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

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

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

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.

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.

Rhizosphere C flux from tree roots to soil: spatial and temporal differences between sugar maple and yellow birch saplings

NASA Astrophysics Data System (ADS)

Phillips, R. P.; Fahey, T. J.

2003-12-01

Rhizosphere carbon flux (RCF) has rarely been measured for intact root-soil systems. We measured RCF for eight year-old saplings of sugar maple (Acer saccharum) and yellow birch (Betula allegheniensis) collected from Hubbard Brook Experimental Forest and transplanted into 35 cm diameter pots with native soil horizons intact. We hypothesized birch roots which support ectomycorrhizal fungi would release more C to the rhizosphere than sugar maple roots which support vesicular-arbuscular mycorrhizal fungi. Saplings (n=5) were pulse-labeled with 13CO2 at ambient CO2 concentrations for 4-6 hours, and the label was chased through rhizosphere and bulk soil pools in organic and mineral horizons for 7 days. We observed immediate appearance of the label in rhizosphere soil, and there was a striking difference in the temporal pattern of 13C concentration between species. In maple, peak concentration of the label appeared at day 1 and declined over time whereas in birch the label increased in concentration over the 7 day chase period. As a result, total RCF was 2-3 times greater from birch roots. We estimate at least 5% and 10% of NPP may be released from this flux pathway in sugar maple and yellow birch saplings respectively. These results suggest that rhizosphere C flux likely represents a substantial proportion of NPP in northern hardwood forests, and may be influenced by trees species and mycorrhizal association.

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

Irrigation Differentially Impacts Populations of Indigenous Antibiotic-Producing Pseudomonas spp. in the Rhizosphere of Wheat

PubMed Central

Mavrodi, Olga V.; Mavrodi, Dmitri V.; Parejko, James A.; Thomashow, Linda S.

2012-01-01

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 Columbia Plateau of the Inland Pacific Northwest. Population sizes and plant colonization frequencies of Phz+ and Phl+ Pseudomonas spp. were determined in winter and spring wheat collected during the growing seasons from 2008 to 2009 from selected commercial dryland and irrigated fields in central Washington State. Only Phz+ bacteria were detected on dryland winter wheat, with populations ranging from 4.8 to 6.3 log CFU g−1 of root and rhizosphere colonization frequencies of 67 to 100%. The ranges of population densities of Phl+ and Phz+ Pseudomonas spp. recovered from wheat grown under irrigation were similar, but 58 to 100% of root systems were colonized by Phl+ bacteria whereas only 8 to 50% of plants harbored Phz+ bacteria. In addition, Phz+ Pseudomonas spp. were abundant in the rhizosphere of native plant species growing in nonirrigated areas adjacent to the sampled dryland wheat fields. This is the first report that documents the impact of irrigation on indigenous populations of two closely related groups of antibiotic-producing pseudomonads that coinhabit the rhizosphere of an economically important cereal crop. These results demonstrate how crop management practices can influence indigenous populations of antibiotic-producing pseudomonads with the capacity to suppress soilborne diseases of wheat. PMID:22389379

Diel plant water use and competitive soil cation exchange interact to enhance NH 4 + and K + availability in the rhizosphere

DOE PAGES

Espeleta, Javier F.; Cardon, Zoe G.; Mayer, K. Ulrich; ...

2016-11-12

Hydro-biogeochemical processes in the rhizosphere regulate nutrient and water availability, and thus ecosystem productivity. We hypothesized that two such processes often neglected in rhizosphere models — diel plant water use and competitive cation exchange — could interact to enhance availability of K + and NH 4 +, both high-demand nutrients. A rhizosphere model with competitive cation exchange was used to investigate how diel plant water use (i.e., daytime transpiration coupled with no nighttime water use, with nighttime root water release, and with nighttime transpiration) affects competitive ion interactions and availability of K + and NH 4 +. Competitive cation exchangemore » enabled lowdemand cations that accumulate against roots (Ca 2+, Mg 2+, Na +) to desorb NH 4 + and K + from soil, generating non-monotonic dissolved concentration profiles (i.e. ‘hotspots’ 0.1–1 cm from the root). Cation accumulation and competitive desorption increased with net root water uptake. Daytime transpiration rate controlled diel variation in NH 4 + and K + aqueous mass, nighttime water use controlled spatial locations of ‘hotspots’, and day-to-night differences in water use controlled diel differences in ‘hotspot’ concentrations. Finally, diel plant water use and competitive cation exchange enhanced NH 4 + and K + availability and influenced rhizosphere concentration dynamics. Demonstrated responses have implications for understanding rhizosphere nutrient cycling and plant nutrient uptake.« less

Is rhizosphere remediation sufficient for sustainable revegetation of mine tailings?

PubMed

Huang, Longbin; Baumgartl, Thomas; Mulligan, David

2012-07-01

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. 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. 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 develop hydro-geochemically stable

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

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.

Amino acid fingerprint in the rhizosphere of Pisum sativum in response to water stress

NASA Astrophysics Data System (ADS)

Bobille, Hélène; Fustec, Joëlle; Robins, Richard J.; Cukier, Caroline; Limami, Anis M.

2017-04-01

In cropping systems, legumes release substantial amounts of nitrogen (N) into the soil, via rhizodeposition, and constitute a sustainable source of N, instead of synthetic N fertilisers (Fustec et al. 2010). More frequent or/and intense droughts and floodings, due to climate change and intensification of agriculture, may affect N rhizodeposition (Preece & Peñuelas 2016). However, the effects of water stress on this process are poorly documented. A part of N derived from root exudates, mainly in amino acids (AAs) form, is suspected shape and regulate rhizosphere microbial community, thus playing a potential role in maintaining plant health in case of abiotic stress (Moe 2013). We hypothesized that root AA exudation could change significantly, according to water availability, and would help to understand N metabolism changes in plant-rhizosphere interactions. Because studying exudation from plant grown in unsterilized soil is challenging (Oburger et al. 2013), we have measured the rhizosphere AA fingerprint (RAAF), as the result of interactions between AA exudation and rhizospheric environment. In addition, plants were stem-labeled (cotton-wick) with 15N-urea for 72 h to provide direct evidence of a link between root AA and exudation in the soil. The RAAF was measured in Pisum sativum rhizosphere, under either a water deficit or a water excess for 72 h. Water deficit decreases biomass accumulation in shoots but not in roots. Then, water deficit had no significant effect on total AAs released into the rhizosphere but, it significantly modified the composition of RAAF, with a preferential increase of proline, alanine and glutamate and a rise in isotopic enrichment of AAs derived from oxaloacetate in tricarboxylic acidic cycle (asparagine, aspartate, threonine and isoleucine). These results support the idea that, under the early stages of water deficit, recently assimilated N is rapidly translocated to the roots, and part of it is exudated in AAs. Most of the exudated

Inactivation of gacS Does Not Affect the Competitiveness of Pseudomonas chlororaphis in the Arabidopsis thaliana Rhizosphere

PubMed Central

Schmidt-Eisenlohr, Heike; Gast, Astrid; Baron, Christian

2003-01-01

Quorum-sensing-controlled processes are considered to be important for the competitiveness of microorganisms in the rhizosphere. They affect cell-cell communication, biofilm formation, and antibiotic production, and the GacS-GacA two-component system plays a role as a key regulator. In spite of the importance of this system for the regulation of various processes, strains with a Gac− phenotype are readily recovered from natural habitats. To analyze the influence of quorum sensing and the influence of the production of the antibiotic phenazine-1-carboxamide on rhizosphere colonization by Pseudomonas chlororaphis, a gnotobiotic system based on Arabidopsis thaliana seedlings in soil was investigated. Transposon insertion mutants of P. chlororaphis isolate SPR044 carrying insertions in different genes required for the production of N-acyl-homoserine lactones and phenazine-1-carboxamide were generated. Analysis of solitary rhizosphere colonization revealed that after prolonged growth, the population of the wild type was significantly larger than that of the homoserine lactone-negative gacS mutant and that of a phenazine-1-carboxamide-overproducing strain. In cocultivation experiments, however, the population size of the gacS mutant was similar to that of the wild type after extended growth in the rhizosphere. A detailed analysis of growth kinetics was performed to explain this phenomenon. After cells grown to the stationary phase were transferred to fresh medium, the gacS mutant had a reduced lag phase, and production of the stationary-phase-specific sigma factor RpoS was strongly reduced. This may provide a relative competitive advantage in cocultures with other bacteria, because it permits faster reinitiation of growth after a change to nutrient-rich conditions. In addition, delayed entry into the stationary phase may allow more efficient nutrient utilization. Thus, GacS-GacA-regulated processes are not absolutely required for efficient rhizosphere colonization in

Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species.

PubMed

Caballero-Mellado, Jesús; Martínez-Aguilar, Lourdes; Paredes-Valdez, Guadalupe; Santos, Paulina Estrada-De los

2004-07-01

It was shown recently that the genus Burkholderia is rich in N2-fixing bacteria that are associated with plants. A group of these diazotrophic isolates with identical or very similar 16S rDNA restriction patterns [designated amplified rDNA restriction analysis (ARDRA) genotypes 13, 14 and 15] was selected and a polyphasic taxonomic study was performed, which included new isolates that were recovered from rhizospheres, rhizoplanes or internal tissues of maize, sugarcane and coffee plants. Morphological, physiological and biochemical features, as well as multi-locus enzyme electrophoresis profiles and whole-cell protein patterns, of 20 strains were analysed. In addition, analysis of cellular fatty acid profiles, 16S rDNA sequence analysis and DNA-DNA reassociation experiments were performed with representative strains. The taxonomic data indicated that the strains analysed belong to a novel diazotrophic Burkholderia species, for which the name Burkholderia unamae sp. nov. is proposed. Strain MTl-641T (=ATCC BAA-744T=CIP 107921T), isolated from the rhizosphere of maize, was designated as the type strain. B. unamae was found as an endophyte of plants grown in regions with climates ranging from semi-hot subhumid to hot humid, but not from plants grown in regions with semi-hot or hot dry climates. Moreover, B. unamae was isolated from rhizospheres and plants growing in soils with pH values in the range 4.5-7.1, but not from soils with pH values higher than 7.5.

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

PubMed

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

2015-01-01

Key concerns in the ecological evaluation of GM crops are undesirably spread, gene flow, other environmental impacts, and consequences on soil microorganism's biodiversity. Numerous reports have highlighted the effects of transgenic plants on the physiology of non-targeted rhizospheric microbes and the food chain via causing adverse effects. Therefore, there is an urgent need to develop transgenics with insignificant toxic on environmental health. In the present study, SUV3 overexpressing salt tolerant transgenic rice evaluated in New Delhi and Cuttack soil conditions for their effects on physicochemical and biological properties of rhizosphere. Its cultivation does not affect soil properties viz., pH, Eh, organic C, P, K, N, Ca, Mg, S, Na and Fe(2+). Additionally, SUV3 rice plants do not cause any change in the phenotype, species characteristics and antibiotic sensitivity of rhizospheric bacteria. The population and/or number of soil organisms such as bacteria, fungi and nematodes were unchanged in the soil. Also, the activity of bacterial enzymes viz., dehydrogenase, invertase, phenol oxidases, acid phosphatases, ureases and proteases was not significantly affected. Further, plant growth promotion (PGP) functions of bacteria such as siderophore, HCN, salicylic acid, IAA, GA, zeatin, ABA, NH3, phosphorus metabolism, ACC deaminase and iron tolerance were, considerably, not influenced. The present findings suggest ecologically pertinent of salt tolerant SUV3 rice to sustain the health and usual functions of the rhizospheric organisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

Field experiment for determining lead accumulation in rice grains of different genotypes and correlation with iron oxides deposited on rhizosphere soil.

PubMed

Lai, Yu-Cheng; Syu, Chien-Hui; Wang, Pin-Jie; Lee, Dar-Yuan; Fan, Chihhao; Juang, Kai-Wei

2018-01-01

Paddy rice (Oryza sativa L.) is a major staple crop in Asia. However, heavy metal accumulation in paddy soil poses a health risk for rice consumption. Although plant uptake of Pb is usually low, Pb concentrations in rice plants have been increasing with Pb contamination in paddy fields. It is known that iron oxide deposits in the rhizosphere influence the absorption of soil Pb by rice plants. In this study, 14 rice cultivars bred in Taiwan, including ten japonica cultivars (HL21, KH145, TC192, TK9, TK14, TK16, TN11, TNG71, TNG84, and TY3) and four indica cultivars (TCS10, TCS17, TCSW2, and TNGS22), were used in a field experiment. We investigated the genotypic variation in rice plant Pb in relation to iron oxides deposited in the rhizosphere, as seen in a suspiciously contaminated site in central Taiwan. The results showed that the cultivars TCSW2, TN11, TNG71, and TNG84 accumulated brown rice Pb exceeding the tolerable level of 0.2mgkg -1 . In contrast, the cultivars TNGS22, TK9, TK14, and TY3 accumulated much lower brown rice Pb (<0.1mgkg -1 ); therefore, they should be prioritized as safe cultivars for sites with potential contamination. Moreover, the iron oxides deposited on the rhizosphere soil show stronger affinity to soil-available Pb than those on the root surface to form iron plaque. The relative tendency of Pb sequestration toward rhizosphere soil was negatively correlated with the Pb concentrations in brown rice. The iron oxides deposited on the rhizosphere soil but not on the root surface to form iron plaque dominate Pb sequestration in the rhizosphere. Therefore, the enhancement of iron oxide deposits on the rhizosphere soil could serve as a barrier preventing soil Pb on the root surface and result in reduced Pb accumulation in brown rice. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of the Entomopathogenic Fungus Beauveria bassiana in the Rhizosphere of Wound-Stressed Zea mays Plants

PubMed Central

McKinnon, Aimee C.; Glare, Travis R.; Ridgway, Hayley J.; Mendoza-Mendoza, Artemio; Holyoake, Andrew; Godsoe, William K.; Bufford, Jennifer L.

2018-01-01

Entomopathogenic fungi from the genus Beauveria (Vuillemin) play an important role in controlling insect populations and have been increasingly utilized for the biological control of insect pests. Various studies have reported that Beauveria bassiana (Bals.), Vuill. also has the ability to colonize a broad range of plant hosts as endophytes without causing disease but while still maintaining the capacity to infect insects. Beauveria is often applied as an inundative spore application, but little research has considered how plant colonization may alter the ability to persist in the environment. The aim of this study was to investigate potential interactions between B. bassiana and Zea mays L. (maize) in the rhizosphere following inoculation, in order to understand the factors that may affect environmental persistence of the fungi. The hypothesis was that different isolates of B. bassiana have the ability to colonize maize roots and/or rhizosphere soil, resulting in effects to the plant microbiome. To test this hypothesis, a two-step nested PCR protocol was developed to find and amplify Beauveria in planta or in soil; based on the translation elongation factor 1-alpha (ef1α) gene. The nested protocol was also designed to enable Beauveria species differentiation by sequence analysis. The impact of three selected B. bassiana isolates applied topically to roots on the rhizosphere soil community structure and function were consequently assessed using denaturing gradient gel electrophoresis (DGGE) and MicroRespTM techniques. The microbial community structure and function were not significantly affected by the presence of the isolates, however, retention of the inocula in the rhizosphere at 30 days after inoculation was enhanced when plants were subjected to intensive wounding of foliage to crudely simulate herbivory. The plant defense response likely changed under wound stress resulting in the apparent recruitment of Beauveria in the rhizosphere, which may be an indirect

Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions.

PubMed

Tian, Yongqiang; Gao, Lihong

2014-11-01

Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.

Connecting Taxon-Specific Microbial Activities to Carbon Cycling in the Rhizosphere

NASA Astrophysics Data System (ADS)

Hungate, B. A.; Morrissey, E.; Schwartz, E.; Dijkstra, P.; Blazewicz, S.; Pett-Ridge, J.; Koch, G. W.; Marks, J.; Koch, B.; McHugh, T. A.; Mau, R. L.; Hayer, M.

2016-12-01

Plant carbon inputs influence microbial growth in the rhizosphere, but the quantitative details of these effects are not well understood, nor are their consequences for carbon cycling in the rhizosphere. With a new pulse of carbon input to soil, which microbial taxa increase their growth rates, and by how much? Do any microbial taxa respond negatively? And how does the extra carbon addition alter the utilization of other resources, including other carbon sources, as well as inorganic nitrogen? This talk will present new research using quantitative stable isotope probing that reveals the distribution of growth responses among microbial taxa, from positive to neutral to negative, and how these growth responses are associated with various substrates. For example, decomposition of soil C in response to added labile carbon occurred as a phylogenetically-diverse majority of taxa shifted toward soil C use for growth. In contrast, bacteria with suppressed growth or that relied directly on glucose for growth clustered strongly by phylogeny. These results suggest that priming is a prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the priming effect in nature. These results also illustrate the potential power of molecular tools and models that seek to estimate metrics directly relevant to quantitative ecology and biogeochemistry, moreso than is the standard currently in microbial ecology. Tools that estimate growth rate, mortality rate, and rates of substrate use - all quantified with the taxonomic precision afforded by modern sequencing - provide a foundation for quantifying the biogeochemical significance of microbial biodiversity, and a more complete understanding of the rich ecosystem of the rhizosphere.

Gene expression profiling of Escherichia coli in response to interactions with the lettuce rhizosphere.

PubMed

Hou, Z; Fink, R C; Black, E P; Sugawara, M; Zhang, Z; Diez-Gonzalez, F; Sadowsky, M J

2012-11-01

The objective of this study was to examine transcriptional changes in Escherichia coli when the bacterium was growing in the lettuce rhizoshpere. A combination of microarray analyses, colonization assays and confocal microscopy was used to gain a more complete understanding of bacterial genes involved in the colonization and growth of E. coli K12 in the lettuce root rhizosphere using a novel hydroponic assay system. After 3 days of interaction with lettuce roots, E. coli genes involved in protein synthesis, stress responses and attachment were up-regulated. Mutants in curli production (crl, csgA) and flagella synthesis (fliN) had a reduced capacity to attach to roots as determined by bacterial counts and by confocal laser scanning microscopy. This study indicates that E. coli K12 has the capability to colonize lettuce roots by using attachment genes and can readily adapt to the rhizosphere of lettuce plants. Results of this study show curli production and biofilm modulation genes are important for rhizosphere colonization and may provide useful targets to disrupt this process. Further studies using pathogenic strains will provide additional information about lettuce-E. coli interactions. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

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

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

Roots and Their Rhizosphere of Fremont Cottonwood and Ponderosa Pine Substantially Stimulated Soil Organic Carbon Decomposition.

NASA Astrophysics Data System (ADS)

Dijkstra, F. A.; Cheng, W.

2006-12-01

There is increasing evidence that living plant roots can significantly alter soil microbial activity and soil organic carbon (SOC) decomposition. Most research on rhizosphere effects on SOC has been done in short-term experiments using annual plants. Here we test if rhizosphere processes of two woody perennial plant species, Fremont cottonwood (Populus fremontii) and Ponderosa pine (Pinus ponderosa), affect SOC decomposition in three different soil types in a 395-day greenhouse experiment. We continuously labeled plants with depleted 13C, which allowed us to separate plant-derived CO2-C from original soil-derived CO2-C in soil respiration measurements. Results show that after 100 days of planting both cottonwood (by 79%) and pine (by 108%) significantly increased soil carbon decomposition compared to soils without plants ("primed C"). We observed no differences in primed C among the three soil types, despite their differences in total and labile carbon and available nitrogen content. Instead, primed C was positively related to foliar biomass. Our results indicate that rhizosphere effects on SOC decomposition play an important role in the carbon cycle of forested ecosystems.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

Rhizosphere microbial communities of canola and wheat at six paired field sites

USDA-ARS?s Scientific Manuscript database

Plant physical and chemical characteristics are known to alter rhizosphere microbial communities, but the effect of introducing canola (Brassica napus L.) into monoculture wheat (Triticum aestivum L.) rotations is not clear. Results from a field study in eastern Washington showed that winter canola ...

Advances in understanding tree fruit-rhizosphere microbiome relationships for enhanced plant health

USDA-ARS?s Scientific Manuscript database

Host-microbe interactions in the rhizosphere influence numerous processes that determine plant productivity and health. The importance of the rhizo-microbiome for plant function is well known, influencing functions ranging from protection of the plant from pathogen attack to enhanced nutrient avail...

Rhizosphere chemical dialogues: plant-microbe interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Badri, D.V.; van der Lelie, D.; Weir, T. L.

2009-12-01

Every organism on earth relies on associations with its neighbors to sustain life. For example, plants form associations with neighboring plants, microflora, and microfauna, while humans maintain symbiotic associations with intestinal microbial flora, which is indispensable for nutrient assimilation and development of the innate immune system. Most of these associations are facilitated by chemical cues exchanged between the host and the symbionts. In the rhizosphere, which includes plant roots and the surrounding area of soil influenced by the roots, plants exude chemicals to effectively communicate with their neighboring soil organisms. Here we review the current literature pertaining to the chemicalmore » communication that exists between plants and microorganisms and the biological processes they sustain.« less

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8

PubMed Central

Hayden, Helen L.; Savin, Keith W.; Wadeson, Jenny; Gupta, Vadakattu V. S. R.; Mele, Pauline M.

2018-01-01

The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R. solani AG8. Analysis of 12 rhizosphere metatranscriptomes (six per field) was undertaken using two bioinformatic approaches involving unassembled and assembled reads. Differential expression analysis showed the dominant taxa in the rhizosphere based on mRNA annotation were Arthrobacter spp. and Pseudomonas spp. for non-suppressive samples and Stenotrophomonas spp. and Buttiauxella spp. for the suppressive samples. The assembled metatranscriptome analysis identified more differentially expressed genes than the unassembled analysis in the comparison of suppressive and non-suppressive samples. Suppressive samples showed greater expression of a polyketide cyclase, a terpenoid biosynthesis backbone gene (dxs) and many cold shock proteins (csp). Non-suppressive samples were characterised by greater expression of antibiotic genes such as non-heme chloroperoxidase (cpo) which is involved in pyrrolnitrin synthesis, and phenazine biosynthesis family protein F (phzF) and its transcriptional activator protein (phzR). A large number of genes involved in detoxifying reactive oxygen species (ROS) and superoxide radicals (sod, cat, ahp, bcp, gpx1, trx) were also expressed in the non-suppressive rhizosphere samples most likely in response to the infection of wheat roots by R

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

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…

Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots.

PubMed

Bressan, Mélanie; Roncato, Marie-Anne; Bellvert, Floriant; Comte, Gilles; Haichar, Feth Zahar; Achouak, Wafa; Berge, Odile

2009-11-01

A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched (13)CO(2) atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.

Ecotoxicological assessment of pesticides and their combination on rhizospheric microbial community structure and function of Vigna radiata.

PubMed

Walvekar, Varsha Ashok; Bajaj, Swati; Singh, Dileep K; Sharma, Shilpi

2017-07-01

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45 days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as "safe alternatives."

Colonization on Cucumber Root and Enhancement of Chlorimuron-ethyl Degradation in the Rhizosphere by Hansschlegelia zhihuaiae S113 and Root Exudates.

PubMed

Zhang, Hao; Chen, Feng; Zhao, Hua-Zhu; Lu, Jia-Sen; Zhao, Meng-Jun; Hong, Qing; Huang, Xing

2018-05-09

The colonization of Hansschlegelia zhihuaiae S113 and its degradation of the herbicide chlorimuron-ethyl in the cucumber rhizosphere was investigated. The results reveal that S113 colonized the cucumber roots (2.14 × 10 5 cells per gram of roots) and were able to survive in the rhizosphere (maintained for 20 d). The root exudates promoted colonization on roots and increased the degradation of chlorimuron-ethyl by S113. Five organic acids in cucumber-root exudates were detected and identified by HPLC. Citric acid and fumaric acid significantly stimulated S113 colonization on cucumber roots, with 18.4 and 15.5% increases, respectively, compared with the control. After irrigation with an S113 solution for 10 days, chlorimuron-ethyl could not be detected in the roots, seedlings, or rhizosphere soil, which allowed for improved cucumber growth. Therefore, the degradation mechanism of chlorimuron-ethyl residues by S113 in the rhizosphere could be applied in situ for the bioremediation of chlorimuron-ethyl contaminated soil to ensure crop safety.

Response of the rhizosphere prokaryotic community of barley (Hordeum vulgare L.) to elevated atmospheric CO2 concentration in open-top chambers.

PubMed

Szoboszlay, Márton; Näther, Astrid; Mitterbauer, Esther; Bender, Jürgen; Weigel, Hans-Joachim; Tebbe, Christoph C

2017-08-01

The effect of elevated atmospheric CO 2 concentration [CO 2 ] on the diversity and composition of the prokaryotic community inhabiting the rhizosphere of winter barley (Hordeum vulgare L.) was investigated in a field experiment, using open-top chambers. Rhizosphere samples were collected at anthesis (flowering stage) from six chambers with ambient [CO 2 ] (approximately 400 ppm) and six chambers with elevated [CO 2 ] (700 ppm). The V4 region of the 16S rRNA gene was PCR-amplified from the extracted DNA and sequenced on an Illumina MiSeq instrument. Above-ground plant biomass was not affected by elevated [CO 2 ] at anthesis, but plants exposed to elevated [CO 2 ] had significantly higher grain yield. The composition of the rhizosphere prokaryotic communities was very similar under ambient and elevated [CO 2 ]. The dominant taxa were Bacteroidetes, Actinobacteria, Alpha-, Gamma-, and Betaproteobacteria. Elevated [CO 2 ] resulted in lower prokaryotic diversity in the rhizosphere, but did not cause a significant difference in community structure. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Application of a redox gradostat reactor for assessing rhizosphere microorganism activity on lambda-cyhalothrin.

PubMed

Peacock, T J; Mikell, A T; Moore, M T; Smith, S

2014-03-01

Bacterial activity on pesticides can lead to decreased toxicity or persistence in aquatic systems. Rhizosphere activity is difficult to measure in situ. To mimic rhizosphere properties of the soft rush, Juncus effusus, a single-stage gradostat reactor was developed to study cycling of lambda-cyhalothrin by rhizobacteria and the effects of Fe(III) and citrate, both common in wetland soil, on lambda-cyhalothrin degradation. Redox gradient changes, greater than ± 10 mV, were apparent within days 5-15 both in the presence and absence of ferric citrate. Through the production of a redox gradient (p < 0.05) by rhizobacteria and the ability to measure pesticide loss over time (p < 0.05), reactors were useful in expanding knowledge on this active environment.

Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China.

PubMed

Lin, Li'an; Liu, Wenwen; Zhang, Manping; Lin, Xiaolan; Zhang, Yihui; Tian, Yun

2018-06-13

In the southernmost part of coast of China, two height forms of Spartina alterniflora, tall and short, have invaded Leizhou Peninsula within the last decade. However, the effect of different height forms of Spartina alterniflora on plant-microbe interaction has not been clarified. Here, the community structures of rhizosphere bacteria and the abundance of N- and S-cycling functional genes associated with selected S. alterniflora were investigated in the field and a common garden. The community structure of tall-form S. alterniflora was distinct from short-form S. alterniflora at OTU level in the field, even after transplantation into a common garden. The abundance of bacterial amoA, nirS, and nosZ in tall S. alterniflora was significantly greater than those in short S. alterniflora in the field; however, this difference disappeared in a 1-year common garden experiment. These results suggested that compared with the tall-form S. alterniflora, the rhizosphere of short-form S. alterniflora harbored fewer nitrification-denitrification related microorganisms, which might benefit from conserving N in an N limited habitat. Together, our results suggested that tall- and short-form S. alterniflora can host their specific rhizosphere microbial communities and had different strategies of N usage via selecting the composition of rhizosphere bacterial assemblages, which in turn might determine the growth and invasiveness of S. alterniflora in its introduced range.

Comparison of rhizosphere properties as affected by different Bt- and non-Bt-cotton (Gossypium hirsutum L.) genotypes and fertilization.

PubMed

Ahamd, Maqshoof; Abbasi, Waleed Mumtaz; Jamil, Moazzam; Iqbal, Muhammad; Hussain, Azhar; Akhtar, Muhammad Fakhar-U-Zaman; Nazli, Farheen

2017-06-01

Incorporation of genetically modified crops in the cropping system raises the need for studying the effect of these crops on the soil ecosystem. The current study aimed to compare the effect of Bacillus thuringiensis (Bt)- and non-Bt-cotton (Gossypium hirsutum L.) genotypes on rhizosphere properties under fertilized and unfertilized soil conditions. One non-Bt-cotton (IUB 75) and four Bt-cotton varieties (IUB-222, MM-58, IUB-13, FH-142) were sown in a Randomized Complete Block Design (RCBD) in a factorial fashion with three replications under unfertilized (T1) and fertilized (T2 at NPK 310-170-110 kg ha -1 ) soil conditions. The culturable soil bacterial population was recorded at flowering, boll opening, and harvesting stages, while other rhizosphere biological and chemical properties were recorded at harvesting. Results revealed that Bt-cotton genotypes IUB-222 and FH-142 showed significantly higher rhizosphere total nitrogen, NH 4 + -N, available phosphorus, and available potassium. Total organic carbon and microbial biomass carbon was also maximum in the rhizosphere of IUB-222 under fertilized conditions. Similarly, bacterial population (CFU g -1 ) at flowering stage and at harvesting was significantly higher in the rhizosphere of IUB-222 as compared to non-Bt- (IUB-75) and other Bt-cotton genotypes under same growth conditions. It showed that Bt genotypes can help in maintaining soil macronutrients (total nitrogen, available phosphorus, and available potassium) under proper nutrient management. Moreover, Bt-cotton genotypes seem to strengthen certain biological properties of the soil, thus increasing the growth and yield capability, maintaining available nutrients in the soil as compared to non-Bt cotton, while no harmful effects of Bt cotton on soil properties was detected.

[Accumulation of S, Fe and Cd in rhizosphere of rice and their uptake in rice with different water managements].

PubMed

Zhang, Xue-Xia; Zhang, Xiao-Xia; Zheng, Yu-Ji; Wang, Rong-Ping; Chen, Neng-Chang; Lu, Pu-Xiang

2013-07-01

The interactions between the concentrations of sulfur, iron and cadmium in the rhizosphere and their uptakes in rice (Oryza sativa L. ) were studied using paddy soil which was contaminated by acid mine drainage under five water-management treatments of 60%, 80%, 100% field moisture capacity (FMC), flooded throughout the entire rice growth period and flooded followed by keeping 80% FMC after heading-flowering period. The water managements had no significant influence on the Fe and Cd concentrations in rhizosphere soil in maturity stage, although the concentration of Cd slightly increased with the increase of soil moisture in the tillering stage. However, the uptake of Fe and Cd in rice was obviously related to water managements. The increase of soil moisture enhanced the uptake of Fe, but decreased the uptake of Cd in different organs of rice (roots, stems and leaves, grains) except for Cd uptake of the root in the 60% FMC treatment. However, aerobic treatment after heading-flowering period enhanced Cd uptake in rice in all treatments, but did not influence the uptake of Fe in rice. On the other hand, the increase of soil moisture reduced the concentrations of total sulfur and available sulfur in the rhizosphere soil except for the 60% FMC treatment, which corresponded with the reduction of Cd uptake in rice. And the aerobic treatment promoted Cd uptake in rice, which was also positively related to the increase of total sulfur and available sulfur in rhizosphere soil. Therefore, it was concluded that the uptake and speciation of sulfur in rhizosphere soil other than the change of Fe concentration induced by water management could play an important role in Cd uptake of rice.

Interaction between 2,4-Diacetylphloroglucinol- and Hydrogen Cyanide-Producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the Tomato Rhizosphere

PubMed Central

Paulin, Mélanie M.; Novinscak, Amy; Lanteigne, Carine; Gadkar, Vijay J.

2017-01-01

ABSTRACT We have previously demonstrated that inoculation of tomato plants with 2,4-diacetylphloroglucinol (DAPG)- and hydrogen cyanide (HCN)-producing Pseudomonas brassicacearum LBUM300 could significantly reduce bacterial canker symptoms caused by Clavibacter michiganensis subsp. michiganensis. In this study, in order to better characterize the population dynamics of LBUM300 in the rhizosphere of tomato plants, we characterized the role played by DAPG and HCN production by LBUM300 on rhizosphere colonization of healthy and C. michiganensis subsp. michiganensis-infected tomato plants. The impact of C. michiganensis subsp. michiganensis presence on the expression of DAPG and HCN biosynthetic genes in the rhizosphere was also examined. In planta assays were performed using combinations of C. michiganensis subsp. michiganensis and wild-type LBUM300 or DAPG (LBUM300ΔphlD) or HCN (LBUM300ΔhcnC) isogenic mutant strains. Populations of LBUM300 and phlD and hcnC gene expression levels were quantified in rhizosphere soil at several time points up to 264 h postinoculation using culture-independent quantitative PCR (qPCR) and reverse transcriptase quantitative PCR (RT-qPCR) TaqMan assays, respectively. The presence of C. michiganensis subsp. michiganensis significantly increased rhizospheric populations of LBUM300. In C. michiganensis subsp. michiganensis-infected tomato rhizospheres, the populations of wild-type LBUM300 and strain LBUM300ΔhcnC, both producing DAPG, were significantly higher than the population of strain LBUM300ΔphlD. A significant upregulation of phlD expression was observed in the presence of C. michiganensis subsp. michiganensis, while hcnC expression was only slightly increased in the mutant strain LBUM300ΔphlD when C. michiganensis subsp. michiganensis was present. Additionally, biofilm production was found to be significantly reduced in strain LBUM300ΔphlD compared to the wild-type and LBUM300ΔhcnC strains. IMPORTANCE The results of this study

Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

PubMed

Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

2011-05-01

The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

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. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-01-01

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

Soil Minerals: AN Overlooked Mediator of Plant-Microbe Competition for Organic Nitrogen in the Rhizosphere

NASA Astrophysics Data System (ADS)

Grandy, S.; Jilling, A.; Keiluweit, M.

2016-12-01

Recent research on the rate limiting steps in soil nitrogen (N) availability have shifted in focus from mineralization to soil organic matter (SOM) depolymerization. To that end, Schimel and Bennett (2004) argued that together with enzymatic breakdown of polymers to monomers, microsite processes and plant-microbial competition collectively drive N cycling. Here we present new conceptual models arguing that while depolymerization is a critical first step, mineral-organic associations may ultimately regulate the provisioning of bioavailable organic N, especially in the rhizosphere. Mineral-associated organic matter (MAOM) is a rich reservoir for N in soils and often holds 5-7x more N than particulate or labile fractions. However, MAOM is considered largely unavailable to plants as a source of N due to the physicochemical forces on mineral surfaces that stabilize organic matter. We argue that in rhizosphere hotspots, MAOM is in fact a potentially mineralizable and important source of nitrogen for plants. Several biochemical strategies enable plants and microbes to compete with mineral-organic interactions and effectively access MAOM. In particular, root-deposited low molecular weight compounds in the form of root exudates facilitate the biotic and abiotic destabilization and subsequent bioavailability of MAOM. We believe that the competitive balance between the potential fates of assimilable organic N — bound to mineral surfaces or dissolved and available for assimilation — depends on the specific interaction between and properties of the clay, soil solution, mineral-bound organic matter, and microbial community. For this reason, the plant-soil-MAOM interplay is enhanced in rhizosphere hotspots relative to non-rhizosphere environments, and likely strongly regulates plant-microbe competition for N. If these hypotheses are true, we need to reconsider potential soil N cycle responses to changes in climate and land use intensity, focusing on the processes by which

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun.

PubMed

Deng, Songqiang; Ke, Tan; Li, Longtai; Cai, Shenwen; Zhou, Yuyue; Liu, Yue; Guo, Limin; Chen, Lanzhou; Zhang, Dayi

2018-06-01

Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH 4 -N, NO 3 -N, NO 2 -N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China.

PubMed

Sun, Xiaoyan; Zhou, Yanling; Tan, Yinjing; Wu, Zhaoxiang; Lu, Ping; Zhang, Guohua; Yu, Faxin

2018-05-25

To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water

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 ...

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

Effects of P and C inputs on microbial activities in P limiting bulk and rhizosphere soil

NASA Astrophysics Data System (ADS)

Bilyera, Nataliya

2017-04-01

Keywords: phosphorus, soil ATP, phosphatase, microbial biomass, Cambisol. Phosphorus (P) is the second important nutrient for plants and limiting element in many ecosystems. P is a non-renewable resource, and based on its current rate of use, it has been estimated that the worlds known reserves of P rocks may be depleted within the current century. Soils with high-sorption P capacity require higher P additions, but, do not provide plants with sufficient available P. Therefore, it is necessary to reduce P application rates, but facilitate soil microbiological activity to maintain good P availability for plants. We aimed to study soil adenosine triphosphate (ATP), microbial biomass (MBC) and phosphatase activity as microbial response to contrasting P input in a low P Cambisol in a 5 days incubation experiment. The treatments were i) bulk soil (no C), ii) rhizosphere soil (10 μg C g-1 soil day-1 - root exudates imitation) and iii) glucose addition to soil (50 μg C g-1 soil - for microbial activation). Three rates of P as KH2PO4 were applied at each C treatments: i) no P (P0) - for P severe limitation; ii) 10% P from initial extractable soil P (P10) - low P input; and iii) 50% P from initial extractable soil P (P50) - high P input. We tested the following hypotheses: 1) the better response of MBC and ATP to P is expected to be in the rhizosphere soil, as continuous C input resulted in gradual microbial activation; 2) phosphatase activity will decrease with increasing P rates in all soils. Microbial biomass grew linear (R2=0.99) and simultaneously with incremental P addition in bulk soil. In rhizosphere and C-amended soils, on contrary, the MBC response to P level was represented by quadratic model (y=-0.06x2+2.84x+37.03; R2=0.93). This model shows the highest MBC value at P23, which indicates optimal and the most effective application rate for this soil type. The correlation between soil ATP content and P rates ascended in the order bulk soil (R2=0.34) > C

Arbuscular mycorrhizal fungal communities in the rhizosphere of a continuous cropping soybean system at the seedling stage.

PubMed

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

Arbuscular mycorrhizae (AM) fungi play a crucial role in the growth of soybean; however, the planting system employed is thought to have an effect on AM fungal communities in the rhizosphere. This study was performed to explore the influence of continuous soybean cropping on the diversity of Arbuscular mycorrhizal (AM) fungi, and to identify the dominant AM fungus during the seedling stage. Three soybean cultivars were planted under two and three years continuous cropping, respectively. The diversity of AM fungi in the rhizosphere soil at the seedling stage was subsequently analyzed using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). The results showed that an increase in cropping years improved the colonization rate of AM in all three soybean cultivars. Moreover, the dominant species were found to be Funneliformis mosseae and Glomus species. The results of cluster analysis further confirmed that the number of years of continuous cropping significantly affected the composition of rhizospheric AM fungal communities in different soybean cultivars. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

[Effects of mulberry/soybean intercropping on the plant growth and rhizosphere soil microbial number and enzyme activities].

PubMed

Hu, Ju-Wei; Zhu, Wen-Xu; Zhang, Hui-Hui; Xu, Nan; Li, Xin; Yue, Bing-Bing; Sun, Guang-yu

2013-05-01

A root separation experiment was conducted to investigate the plant growth and rhizosphere soil microbes and enzyme activities in a mulberry/soybean intercropping system. As compared with those in plastic barrier and nylon mesh barrier treatments, the plant height, leaf number, root length, root nodule number, and root/shoot ratio of mulberry and soybean in non-barrier treatment were significantly higher, and the soybean's effective nodule number was larger. The available phosphorous content in the rhizosphere soils of mulberry and soybean in no barrier and nylon mesh barrier treatments was increased by 10.3% and 11.1%, and 5.1% and 4.6%, respectively, as compared with that in plastic barrier treatment. The microbial number, microbial diversity, and enzyme activities in the rhizosphere soils of mulberry and soybean were higher in the treatments of no barrier and nylon mesh barrier than in the treatment of plastic barrier. All the results indicated that there was an obvious interspecific synergistic effect between mulberry and soybean in the mulberry/soybean intercropping system.

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

[Effects of biochar and sheep manure on rhizospheric soil microbial community in continuous ratooning tea orchards].

PubMed

Li, Yan Chun; Li, Zhao Wei; Lin, Wei Wei; Jiang, Yu Hang; Weng, Bo Qi; Lin, Wen Xiong

2018-04-01

Long-term continuous ratooning of tea could lead to serious soil acidification, nutritional imbalance, and the deterioration of the rhizosphere micro-ecological environment. Understanding the effects of biochar and sheep manure on the growth of tea plants and the rhizosphere microbial community structure and function would provide theoretical basis to improve the soil micro-ecological environment of continuous ratooning tea orchards. Biolog technology combined with phospholipid fatty acid (PLFA) approaches were employed to quantify the effects of biochar (40 t·hm -2 ) and sheep manure on the growth of 20 years continuous ratooning tea plants, soil chemical properties, and the soil microbial community structure and function. The results showed that after one year treatment, biochar and sheep manure both improved soil pH and nutrition, and significantly enhanced tea production. Compared with the routine fertilizer application (CK), the biochar and sheep manure treatments significantly increased the carbon metabolic activity (AWCD) and microorganism diversity in the rhizosphere soils, and increased the relative utilization of the carbon sources such as amines, carbohydrates, and polymers. The total PLFA concentrations in the biochar and sheep manure treatments were significantly increased by 20.9% and 47.5% than that in the routine fertilizers application. In addition, sheep manure treatment significantly decreased the saturated/monosaturated fatty acids In conclusion, biochar and sheep manure could alleviate soil acidification, enhance soil nutrition and the growth of tea plants. Both management strategies could increase the soil microbial activity and biomass, enhance the diversity, and improve the microbial community structure, which could be taken as effective measures to regulate the rhizosphere micro-environment of tea plants.

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

PubMed

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

2013-12-01

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. © 2013 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Spatially Resolved Carbon Isotope and Elemental Analyses of the Root-Rhizosphere-Soil System to Understand Below-ground Nutrient Interactions

NASA Astrophysics Data System (ADS)

Denis, E. H.; Ilhardt, P.; Tucker, A. E.; Huggett, N. L.; Rosnow, J. J.; Krogstad, E. J.; Moran, J.

2017-12-01

The intimate relationships between plant roots, rhizosphere, and soil are fostered by the release of organic compounds from the plant (through various forms of rhizodeposition) into soil and the simultaneous harvesting and delivery of inorganic nutrients from the soil to the plant. This project's main goal is to better understand the spatial controls on bi-directional nutrient exchange through the rhizosphere and how they impact overall plant health and productivity. Here, we present methods being developed to 1) spatially track the release and migration of plant-derived organics into the rhizosphere and soil and 2) map the local inorganic geochemical microenvironments within and surrounding the rhizosphere. Our studies focused on switchgrass microcosms containing soil from field plots at the Kellogg Biological Station (Hickory Corners, Michigan), which have been cropped with switchgrass for nearly a decade. We used a 13CO2 tracer to label our samples for both one and two diel cycles and tracked subsequent movement of labeled organic carbon using spatially specific δ13C analysis (with 50 µm resolution). The laser ablation-isotope ratio mass spectrometry (LA-IRMS) approach allowed us to map the extent of 13C-label migration into roots, rhizosphere, and surrounding soil. Preliminary results show the expected decrease of organic exudates with distance from a root and that finer roots (<0.1 mm) incorporated more 13C-label than thicker roots, which likely correlates to specific root growth rates. We are adapting both laser induced breakdown spectroscopy (LIBS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to spatially map inorganic nutrient content in the exact same samples used for LA-IRMS analysis. Both of these methods provide rapid surface mapping of a wide range of elements (with high dynamic range) at 150 μm spatial resolution. Preliminary results show that, based on elemental content, we can distinguish between roots, rhizosphere

[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

Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

DOE PAGES

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

2015-02-11

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

DOE PAGES

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

2015-04-30

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome

PubMed Central

Mavrodi, Dmitri V.; Mavrodi, Olga V.; Elbourne, Liam D. H.; Tetu, Sasha; Bonsall, Robert F.; Parejko, James; Yang, Mingming; Paulsen, Ian T.; Weller, David M.; Thomashow, Linda S.

2018-01-01

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables

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

PubMed Central

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

2016-01-01

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

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.

Assessment of SCAR markers to design real-time PCR primers for rhizosphere quantification of Azospirillum brasilense phytostimulatory inoculants of maize.

PubMed

Couillerot, O; Poirier, M-A; Prigent-Combaret, C; Mavingui, P; Caballero-Mellado, J; Moënne-Loccoz, Y

2010-08-01

To assess the applicability of sequence characterized amplified region (SCAR) markers obtained from BOX, ERIC and RAPD fragments to design primers for real-time PCR quantification of the phytostimulatory maize inoculants Azospirillum brasilense UAP-154 and CFN-535 in the rhizosphere. Primers were designed based on strain-specific SCAR markers and were screened for successful amplification of target strain and absence of cross-reaction with other Azospirillum strains. The specificity of primers thus selected was verified under real-time PCR conditions using genomic DNA from strain collection and DNA from rhizosphere samples. The detection limit was 60 fg DNA with pure cultures and 4 x 10(3) (for UAP-154) and 4 x 10(4) CFU g(-1) (for CFN-535) in the maize rhizosphere. Inoculant quantification was effective from 10(4) to 10(8) CFU g(-1) soil. BOX-based SCAR markers were useful to find primers for strain-specific real-time PCR quantification of each A. brasilense inoculant in the maize rhizosphere. Effective root colonization is a prerequisite for successful Azospirillum phytostimulation, but cultivation-independent monitoring methods were lacking. The real-time PCR methods developed here will help understand the effect of environmental conditions on root colonization and phytostimulation by A. brasilense UAP-154 and CFN-535.

Phytate addition to soil induces changes in the abundance and expression of Bacillus β-propeller phytase genes in the rhizosphere.

PubMed

Jorquera, Milko A; Saavedra, Nicolás; Maruyama, Fumito; Richardson, Alan E; Crowley, David E; del C Catrilaf, Rosa; Henriquez, Evelyn J; de la Luz Mora, María

2013-02-01

Phytate-mineralizing rhizobacteria (PMR) perform an essential function for the mineralization of organic phosphorus but little is known about their ecology in soils and rhizosphere. In this study, PCR-based methods were developed for detection and quantification of the Bacillus β-propeller phytase (BPP) gene. Experiments were conducted to monitor the presence and persistence of a phytate-mineralizing strain, Bacillus sp. MQH19, after inoculation of soil microcosms and within the rhizosphere. The occurrence of the BPP gene in natural pasture soils from Chilean Andisols was also examined. The results showed that the Bacillus BPP gene was readily detected in sterile and nonsterile microcosms, and that the quantitative PCR (qPCR) methods could be used to monitor changes in the abundance of the BPP gene over time. Our results also show that the addition of phytate to nonsterile soils induced the expression of the BPP gene in the rhizosphere of ryegrass and the BPP gene was detected in all pasture soils sampled. This study shows that phytate addition soils induced changes in the abundance and expression of Bacillus BPP to genes in the rhizosphere and demonstrates that Bacillus BPP gene is cosmopolitan in pasture soils from Chilean Andisols. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

PubMed

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

2016-07-13

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

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health

PubMed Central

Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality. PMID:29451918

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health.

PubMed

Zhao, Jia; Liu, Jiang; Liang, Hong; Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao; Wang, Yuguo

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality.

p-Coumaric acid influenced cucumber rhizosphere soil microbial communities and the growth of Fusarium oxysporum f.sp. cucumerinum Owen.

PubMed

Zhou, Xingang; Wu, Fengzhi

2012-01-01

Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood. The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1-1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil. These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities.

Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the Rhizosphere of the Arsenic-Hyperaccumulating Plant Pteris vittata L. ▿ †

PubMed Central

Xiong, Jinbo; Wu, Liyou; Tu, Shuxin; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Wang, Gejiao

2010-01-01

To understand how microbial communities and functional genes respond to arsenic contamination in the rhizosphere of Pteris vittata, five soil samples with different arsenic contamination levels were collected from the rhizosphere of P. vittata and nonrhizosphere areas and investigated by Biolog, geochemical, and functional gene microarray (GeoChip 3.0) analyses. Biolog analysis revealed that the uncontaminated soil harbored the greatest diversity of sole-carbon utilization abilities and that arsenic contamination decreased the metabolic diversity, while rhizosphere soils had higher metabolic diversities than did the nonrhizosphere soils. GeoChip 3.0 analysis showed low proportions of overlapping genes across the five soil samples (16.52% to 45.75%). The uncontaminated soil had a higher heterogeneity and more unique genes (48.09%) than did the arsenic-contaminated soils. Arsenic resistance, sulfur reduction, phosphorus utilization, and denitrification genes were remarkably distinct between P. vittata rhizosphere and nonrhizosphere soils, which provides evidence for a strong linkage among the level of arsenic contamination, the rhizosphere, and the functional gene distribution. Canonical correspondence analysis (CCA) revealed that arsenic is the main driver in reducing the soil functional gene diversity; however, organic matter and phosphorus also have significant effects on the soil microbial community structure. The results implied that rhizobacteria play an important role during soil arsenic uptake and hyperaccumulation processes of P. vittata. PMID:20833780

Assessment of the rhizosphere competency and pentachlorophenol-metabolizing activity of a pesticide-degrading strain of Trichoderma harzianum introduced into the root zone of corn seedlings.

PubMed

Rigot, Jerĵme; Matsumura, Fumio

2002-05-01

To develop a dependable approach to introduce laboratory selected, pesticide-degrading microorganisms into soil environments for the purpose of in situ bioremediation, we tested the possibility of utilizing plant rhizospheres as the vehicle. We first established the rhizosphere competency of a strain of the soil fungus Trichoderma harzianum, a biocontrol species well studied by plant pathologists to colonize plant rhizosphere in many parts of the world. The strain we chose, T.h.2023 is resistant to many fungicides, and it has been shown to metabolize several pesticides. Second, we found that it readily metabolized pentachlorophenol (PCP), which is quickly and stochiometrically converted to pentachloroanisole (PCA) in liquid culture. Taking advantage of this specific feature, we have developed a sensitive metabolic marker approach that allowed us to monitor for the continuous presence and activity of this fungal strain in the corn rhizosphere soil in situ over time.

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

Diversity and activity of biosurfactant-producing Pseudomonas in the rhizosphere of black pepper in Vietnam.

PubMed

Tran, H; Kruijt, M; Raaijmakers, J M

2008-03-01

Phytophthora capsici is a major pathogen of black pepper and zoospores play an important role in the infection process. Fluorescent pseudomonads that produce biosurfactants with zoosporicidal activities were isolated from the black pepper rhizosphere in Vietnam, and their genotypic diversity and potential to control Phy. capsici root rot was determined. Biosurfactant-producing pseudomonads were genotypically and biochemically characterized by BOX-polymerase chain reaction (PCR), 16S-rDNA sequencing, reverse-phase-high-performance liquid chromatography and liquid chromatography-mass spectrometry analyses. Biosurfactant-producing fluorescent pseudomonads make up c. 1.3% of the culturable Pseudomonas population in the rhizosphere of black pepper. Although BOX-PCR revealed substantial genotypic diversity, the isolates were shown to produce the same biosurfactants and were all identified as Pseudomonas putida. When applied to black pepper stem cuttings, several of the biosurfactant-producing strains provided significant disease control. In absence of the disease, several of the bacterial strains promoted shoot and root growth of black pepper stem cuttings. Biosurfactant-producing pseudomonads indigenous to the rhizosphere of black pepper plants are genotypically diverse and provide a novel resource for the control of Phy. capsici root rot and growth promotion of black pepper stem cuttings. The results of this study provide a strong basis for further development of supplementary strategies with antagonistic bacteria to control foot and root rot of black pepper and to promote plant growth.

Characterization of a selenium-tolerant rhizosphere strain from a novel Se-hyperaccumulating plant Cardamine hupingshanesis.

PubMed

Tong, Xinzhao; Yuan, Linxi; Luo, Lei; Yin, Xuebin

2014-01-01

A novel selenium- (Se-) hyperaccumulating plant, Cardamine hupingshanesis, accumulating Se as a form of SeCys2, was discovered in Enshi, Hubei, China, which could not be explained by present selenocysteine methyltransferase (SMT) theory. However, it is interesting to investigate if rhizosphere bacteria play some roles during SeCys2 accumulation. Here, one Se-tolerant rhizosphere strain, Microbacterium oxydans, was isolated from C. hupingshanesis. Phylogenetic analysis and 16S rRNA gene sequences determined the strain as a kind of Gram positive bacillus and belonged to the family Brevibacterium frigoritolerans. Furthermore, Se tolerance test indicated the strain could grow in extreme high Se level of 15.0 mg Se L(-1). When exposed to 1.5 mg Se L(-1), SeCys2 was the predominant Se species in the bacteria, consistent with the Se species in C. hupingshanesis. This coincidence might reveal that this strain played some positive effect in SeCys2 accumulation of C. hupingshanesis. Moreover, when exposed to 1.5 mg Se L(-1) or 15.0 mg Se L(-1), As absorption diminished in the logarithmic phase. In contrast, As absorption increased when exposed to 7.5 mg Se L(-1), indicating As metabolism processes could be affected by Se on this strain. The present study provided a sight on the role of rhizosphere bacteria during Se accumulation for Se-hyperaccumulating plant.

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere

PubMed Central

Vacheron, Jordan; Dubost, Audrey; Chapulliot, David; Prigent-Combaret, Claire

2017-01-01

ABSTRACT We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system). PMID:28408666

Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere.

PubMed

Kolton, Max; Graber, Ellen R; Tsehansky, Ludmila; Elad, Yigal; Cytryn, Eddie

2017-02-01

The 'biochar effect' depicts a phenomenon in which biochar soil amendment enhances plant performance by promoting growth and suppressing disease. Although this phenomenon has been observed in numerous studies, the mode of action that explains it is currently unknown. In order to elucidate mechanisms responsible for the 'biochar effect', we comprehensively monitored tomato plant development and resistance to the foliar fungal pathogen Botrytis cinerea, in biochar-amended and nonamended soils using native biochar and washed biochar, striped of labile chemical constituents. We concomitantly assessed bacterial community succession in the rhizosphere by high-throughput 16S rRNA gene amplicon sequencing and carbon-source utilization profiling. Biochar had little impact on plant physiological parameters. However, both native and washed biochar treatments were characterized by higher rhizosphere bacterial diversity and enhanced carbohydrate and phenolic compound utilization rates coupled to stimulation of bacteria known to degrade phenolic compounds. This study indicates that the 'biochar effect' is at least partially dictated by increased diversity and changes in metabolic potential in the rhizosphere microbiome, which is primarily triggered by the recalcitrant carbon backbone of the biochar and tightly bound compounds. It corresponds to the growing consensus that soil amendments which enhance microbial diversity have important benefits to ecosystem functioning. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Identification of β-propeller phytase-encoding genes in culturable Paenibacillus and Bacillus spp. from the rhizosphere of pasture plants on volcanic soils.

PubMed

Jorquera, Milko A; Crowley, David E; Marschner, Petra; Greiner, Ralf; Fernández, María Teresa; Romero, Daniela; Menezes-Blackburn, Daniel; De La Luz Mora, María

2011-01-01

Phytate is one of the most abundant sources of organic phosphorus (P) in soils, but must be mineralized by phytase-producing bacteria to release P for plant uptake. Microbial inoculants based on Bacillus spp. have been developed commercially, but few studies have evaluated the ecology of these bacteria in the rhizosphere or the types of enzymes that they produce. Here, we studied the diversity of aerobic endospore-forming bacteria (EFB) with the ability to mineralize phytate in the rhizosphere of pasture plants grown in volcanic soils of southern Chile. PCR methods were used to detect candidate phytase-encoding genes and to identify EFB bacteria that carry these genes. This study revealed that the phytate-degrading EFB populations of pasture plants included species of Paenibacillus and Bacillus, which carried genes encoding β-propeller phytase (BPP). Assays of enzymatic activity confirmed the ability of these rhizosphere isolates to degrade phytate. The phytase-encoding genes described here may prove valuable as molecular markers to evaluate the role of EFB in organic P mobilization in the rhizosphere. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohseni, Hooman; Agahi, Massoud H.; Razeghi, Manijeh

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 spectramore » 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.« less

Crown-To-Rhizosphere Carbon Transfer In A Temperate Mixed Forest

NASA Astrophysics Data System (ADS)

Siegwolf, R. T.; Steinmann, K.; Saurer, M.; Koerner, C.

2005-12-01

Flux measurements across a range of (managed) European forests showed that ecosystem respiration amounts up to 80 percent of gross primary production (Janssens et al. 2001), the rest is in large sequestered into biomass. According to Malhi et al. (1999) soil respiration accounts for 60-70 percent of total forest ecosystem respiration. A considerable part is released as CO2 via belowground plant component (autotrophic) and soil micro-organism (heterotrophic) respiration. Recent studies on the autotrophic and heterotrophic respiratory fluxes indicate that the proportion of the autotrophic respiration was most likely underestimated (Hoegberg et al, 2001). Furthermore, highly diverging lengths of time have been estimated between the synthesis of carbohydrates and their availability in the rhizosphere. The goal of the presented study was to i) estimate the transport time for new photosynthates from the leaves to the rhizosphere, ii) determine the spatial distribution of these products, and iii) detect a seasonal course in the autotrophic and heterotrophic respiration of freshly formed assimilates. This study was carried out in a temperate mixed forest (The Swiss Canopy Crane Project in Hofstetten near Basel, Switzerland, cf. Pepin and Koerner 2002, Koerner et al, 2005), exposed to an elevated mean CO2 concentration of 530 ppm. The added CO2 originated from fossil fuel combustion and was depleted in 13C, thus serving as an ideal tracer. Based on the isotopic signature of the soil CO2 it was shown that freshly assimilated carbohydrates were transferred to the rhizosphere within ca. 5 days. The spatial variability was considerable and could mostly be explained with the varying tree population, whereas, the broad-leafed area revealed a more negative d13C value than the conifers. A distinct seasonal course in soil ?13C of the CO2 concentration indicated a seasonal variation in the crown-to-rhizosphere carbon transfer Steinmann et al (2004). Hoegberg P, et al. (2001) Large

p-Coumaric Acid Influenced Cucumber Rhizosphere Soil Microbial Communities and the Growth of Fusarium oxysporum f.sp. cucumerinum Owen

PubMed Central

Zhou, Xingang; Wu, Fengzhi

2012-01-01

Background Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood. Methodology/Principal Findings The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1–1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil. Conclusions/Significance These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities. PMID:23118972

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

Root-induced changes of Zn and Pb dynamics in the rhizosphere of sunflower with different plant growth promoting treatments in a heavily contaminated soil.

PubMed

Mousavi, Seyed Majid; Motesharezadeh, Babak; Hosseini, Hossein Mirseyed; Alikhani, Hoseinali; Zolfaghari, Ali Asghar

2018-01-01

Root induced changes are deemed to have an important role in the success of remediation techniques in contaminated soils. Here, the effects of two nano-particles [SiO 2 and zeolite] with an application rate of 200mgkg -1 , and two bacteria [Bacillus safensis FO-036b(T) and Pseudomonas fluorescens p.f.169] in the rhizosphere of sunflower on Zn and Pb dynamics were studied in greenhouse conditions. The treatments reduced the exchangeable Zn (from 13.68% to 30.82%) and Pb (from 10.34% to 25.92%) in the rhizosphere compared to the control. The EC and microbial respiration/population of the rhizosphere and bulk soil had an opposite trend with the exchangeable fraction of Zn and Pb, but dissolved organic carbon followed a similar trend with the more bioavailable fractions. As a result, the accumulation of Pb and Zn in the plant tissues was significantly (p < 0.05) reduced by the application of amendments, which might be due to the shift of the metals to immobile forms induced by the nature of the treatments and changes in the rhizosphere process. The empirical conditions of this research produced the intensification of the rhizosphere process because the findings highlight those changes in the rhizosphere EC, pH and dissolved organic carbon can affect the efficiency of zeolite/SiO 2 NPs and bacteria to immobilize Pb and Zn in the soil, depending on the chemical character of the metals and the treatments. Generally, the affinity of the biotic treatment for Pb was more than the abiotic and conversely, the abiotic treatment showed a higher ability to immobilize Zn than the biotic treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil

PubMed Central

Zhu, Chen; Ling, Ning; Guo, Junjie; Wang, Min; Guo, Shiwei; Shen, Qirong

2016-01-01

The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC–MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on

Mixed Phenolic Acids Mediated Proliferation of Pathogens Talaromyces helicus and Kosakonia sacchari in Continuously Monocultured Radix pseudostellariae Rhizosphere Soil

PubMed Central

Wu, Hongmiao; Wu, Linkun; Wang, Juanying; Zhu, Quan; Lin, Sheng; Xu, Jiahui; Zheng, Cailiang; Chen, Jun; Qin, Xianjin; Fang, Changxun; Zhang, Zhixing; Azeem, Saadia; Lin, Wenxiong

2016-01-01

Radix pseudostellariae L. is a common and popular Chinese medication. However, continuous monoculture has increased its susceptibility to severe diseases. We identified two pathogenic microorganisms, Talaromyces helicus M. (KU355274) and Kosakonia sacchari W. (KU324465), and their antagonistic bacterium, Bacillus pumilus Z. in rhizosphere soil of continuously monocultured R. pseudostellariae. Nine types of phenolic acids were identified both in the rhizosphere soil and in culture medium under sterile conditions. A syringic acid and phenolic acid mixture significantly promoted the growth of T. helicus and K. sacchari. T. helicus could utilize eight types of phenolic acids, whereas K. sacchari could only use four phenolic acids. K. sacchari produced protocatechuic acid when consuming vanillin. Protocatechuic acid negatively affected the growth of B. pumilus. The 3A-DON toxin produced by T. helicus promoted the growth of K. sacchari and inhibited growth of B. pumilus at low concentrations. These data help explain why phenolic exudates mediate a microflora shift and structure disorder in the rhizosphere soil of continuously monocultured R. pseudostellariae and lead to increased replanting disease incidence. PMID:27014250

Nanoparticle-based measurements of pH and O2 dynamics in the rhizosphere of Zostera marina L.: effects of temperature elevation and light-dark transitions.

PubMed

Elgetti Brodersen, Kasper; Koren, Klaus; Lichtenberg, Mads; Kühl, Michael

2016-07-01

Seagrasses can modulate the geochemical conditions in their immediate rhizosphere through the release of chemical compounds from their below-ground tissue. This is a vital chemical defence mechanism, whereby the plants detoxify the surrounding sediment. Using novel nanoparticle-based optical O2 and pH sensors incorporated in reduced and transparent artificial sediment, we investigated the spatio-temporal dynamics of pH and O2 within the entire rhizosphere of Zostera marina L. during experimental manipulations of light and temperature. We combined such measurements with O2 microsensor measurements of the photosynthetic productivity and respiration of seagrass leaves. We found pronounced pH and O2 microheterogeneity within the immediate rhizosphere of Z. marina, with higher below-ground tissue oxidation capability and rhizoplane pH levels during both light exposure of the leaf canopy and elevated temperature, where the temperature-mediated stimuli of biogeochemical processes seemed to predominate. Low rhizosphere pH microenvironments appeared to correlate with plant-derived oxic microzones stimulating local sulphide oxidation and thus driving local proton generation, although the rhizoplane pH levels generally where much higher than the bulk sediment pH. Our data show that Z. marina can actively alter its rhizosphere pH microenvironment alleviating the local H2 S toxicity and enhancing nutrient availability in the adjacent sediment via geochemical speciation shift. © 2016 John Wiley & Sons Ltd.

Characterization of a Selenium-Tolerant Rhizosphere Strain from a Novel Se-Hyperaccumulating Plant Cardamine hupingshanesis

PubMed Central

Yuan, Linxi; Luo, Lei; Yin, Xuebin

2014-01-01

A novel selenium- (Se-) hyperaccumulating plant, Cardamine hupingshanesis, accumulating Se as a form of SeCys2, was discovered in Enshi, Hubei, China, which could not be explained by present selenocysteine methyltransferase (SMT) theory. However, it is interesting to investigate if rhizosphere bacteria play some roles during SeCys2 accumulation. Here, one Se-tolerant rhizosphere strain, Microbacterium oxydans, was isolated from C. hupingshanesis. Phylogenetic analysis and 16S rRNA gene sequences determined the strain as a kind of Gram positive bacillus and belonged to the family Brevibacterium frigoritolerans. Furthermore, Se tolerance test indicated the strain could grow in extreme high Se level of 15.0 mg Se L−1. When exposed to 1.5 mg Se L−1, SeCys2 was the predominant Se species in the bacteria, consistent with the Se species in C. hupingshanesis. This coincidence might reveal that this strain played some positive effect in SeCys2 accumulation of C. hupingshanesis. Moreover, when exposed to 1.5 mg Se L−1 or 15.0 mg Se L−1, As absorption diminished in the logarithmic phase. In contrast, As absorption increased when exposed to 7.5 mg Se L−1, indicating As metabolism processes could be affected by Se on this strain. The present study provided a sight on the role of rhizosphere bacteria during Se accumulation for Se-hyperaccumulating plant. PMID:25478582

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

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

DTIC Science & Technology

1988-04-01

acids. Acetic acid postulated as agent Thalassia Nitrogen fixation in Capone 1983 testudinwn rhizosphere and phyllosphere 13. Fungi living in the...microbial population associated with the rhizome detritus. 26. Durako and Moffler (1987) examined responses of Thalassia testudinum to nitrogen enrichment...economy of seagrasses for communities of Thalassia testudinium and Zostera maina. He concluded that nitrogen fixation is probably more important for

Impact of transgenic Cry1Ac + CpTI cotton on diversity and dynamics of rhizosphere bacterial community of different root environments.

PubMed

Li, Peng; Li, Yongchun; Shi, Jialiang; Yu, Zhibo; Pan, Aihu; Tang, Xueming; Ming, Feng

2018-05-08

The objective of this study was to characterize the diversity and dynamics of rhizosphere bacterial community, especially the response of dominant and rare bacterial taxa to the cultivation of Bt cotton for different root environments at different growth stages. qPCR analyses indicated that bacterial abundances of the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different at seedling and bolling stages. But no significant differences were detected between the same root zones from Bt and the conventional cotton varieties. Total bacterial genera had similar pattern with dominant genera in abundance, and with rare genera in richness to the changes of bacterial community, respectively. Although the rhizosphere bacterial diversity of the three cotton varieties changed in taproot and lateral root, no significant differences were detected in the same root environments between Bt and conventional cotton. Moreover, Soil pH was more correlated with variations in the bacterial community composition than Bt proteins. In conclusion, these results revealed no indication that rhizosphere bacterial community of Bt cotton had different response to increased Bt protein regarding the same root environment. In particular, dominant and rare bacterial taxa showed the variation in diversity and community composition in different root microhabitats. Copyright © 2018. Published by Elsevier B.V.

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.

[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.

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

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery.

PubMed

Jiang, Jie; Pan, Chaohu; Xiao, Aiping; Yang, Xiai; Zhang, Guimin

2017-05-01

Six bacteria strains from heavy-metal-polluted ramie rhizosphere soil were isolated through Cd 2+ stress, which were numbered as JJ1, JJ2, JJ10, JJ11, JJ15, and JJ18. Sequence alignment and phylogenic analysis showed that strain JJ1 belonged to Pseudomonas, strain JJ2 belonged to Cupriavidus, strains JJ11 and JJ15 belonged to Bacillus, and strains JJ10 and JJ18 belonged to Acinetobacter. The tolerance capability of all the strains was the trend of Pb 2+  > Zn 2+  > Cu 2+  > Cd 2+ , the maximum tolerance concentration to Cd 2+ was 200 mg/L, to Pb 2+ was 1600 mg/L, to Zn 2+ was 600 mg/L, and to Cu 2+ was 265 mg/L. Strains JJ1, JJ11, JJ15, and JJ18 could grow well under pH 9.0, and strains JJ2, JJ11, and JJ18 could grow well under 7% of NaCl. The results showed that as a whole these strains had high environmental adaptability. This is the first report that heavy-metal-tolerant bacteria were found from ramie rhizosphere soil, which could be as a foundation to discover the relationship between ramie, rhizosphere bacteria and heavy metals.

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3.

PubMed

Wang, Peng; Marsh, Ellen L; Ainsworth, Elizabeth A; Leakey, Andrew D B; Sheflin, Amy M; Schachtman, Daniel P

2017-11-03

Rising atmospheric concentrations of CO 2 and O 3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO 2 and O 3 (eCO 2 and eO 3 ) the endosphere, rhizosphere and soil were sampled from soybeans under eCO 2 and maize under eO 3 . The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO 2 , associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO 3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO 2 and O 3 .

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...

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

Brevibacillus sp. KUMAs2, a bacterial isolate for possible bioremediation of arsenic in rhizosphere.

PubMed

Mallick, Ivy; Hossain, Sk Tofajjen; Sinha, Sangram; Mukherjee, Samir Kumar

2014-09-01

Arsenic (As) contamination of soil and water has been considered as a major global environmental issue during last few decades. Among the various methods so far reported for reclamation of As contaminated rhizosphere soil, bioremediation using bacteria has been found to be most promising. An As resistant bacterial isolate Brevibacillus sp. KUMAs2 was obtained from As contaminated soil of Nadia, West Bengal, India, which could resist As(V) and As(III) a maximum of 265mM and 17mM, respectively. The strain could remove ~40 percent As under aerobic culture conditions. As resistant property in KUMAs2 was found to be plasmid-borne, which carried both As oxidizing and reducing genes. The strain could promote chilli plant growth under As contaminated soil environment by decreasing As accumulation in plant upon successful colonization in the rhizosphere, which suggests the possibility of using this isolate for successful bioremediation of As in the crop field. Copyright © 2014 Elsevier Inc. All rights reserved.

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

Genetic and functional characterization of culturable plant-beneficial actinobacteria associated with yam rhizosphere.

PubMed

Arunachalam Palaniyandi, Sasikumar; Yang, Seung Hwan; Damodharan, Karthiyaini; Suh, Joo-Won

2013-12-01

Actinobacteria were isolated from the rhizosphere of yam plants from agricultural fields from Yeoju, South Korea and analyzed for their genetic and plant-beneficial functional diversity. A total of 29 highly occurring actinobacterial isolates from the yam rhizosphere were screened for various plant-beneficial traits such as antimicrobial activity on fungi and bacteria; biocontrol traits such as production of siderophore, protease, chitinase, endo-cellulase, and β-glucanase. The isolates were also screened for plant growth-promoting (PGP) traits such as auxin production, phosphate solubilization, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and in vitro Arabidopsis growth promotion. 16S rDNA sequence-based phylogenetic analysis was carried out on the actinobacterial isolates to determine their genetic relatedness to known actinobacteria. BOX-PCR analysis revealed high genetic diversity among the isolates. Several isolates were identified to belong to the genus Streptomyces and a few to Kitasatospora. The actinobacterial strains exhibited high diversity in their functionality and were identified as novel and promising candidates for future development into biocontrol and PGP agents. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing.

PubMed

Han, Cheng; Liu, Biao; Zhong, Wenhui

2018-05-30

This study aimed to investigate the influence of planting Cry1Ab/Cry1Ac gene expressing rice (Bt rice) on rhizospheric active methanogenic archaeal communities. The non-transgenic parental line was used as the control (Ck rice). DNA-based stable isotope probing (DNA-SIP) technology traced the rhizospheric active methanogens at the tillering stage. The results revealed significantly lower CH 4 emission flux from Bt soil than that from Ck soil during the whole growth period. The active methanogenic community composition remained stable. The RC-I lineage (77.9-79.8%) and Methanosaetaceae (13.9-15.1%) were the predominant active methanogens in Bt and Ck rice rhizospheres. However, the abundance of functionally active methanogens in the Bt rice rhizosphere was significantly reduced. Lower levels of root exudates (that included carbohydrate and organic acids) from Bt rice were also detected at the tillering stage. This study found that the genetic modification of rice reduced the potential methanogenic substrates came from plant-derived root exudates, which represented an important factor in reducing CH 4 generation and active methanogenic archaeal abundance in Bt rhizosphere soil. The effect of genetically modified (GM) insect-resistant crops on soil microorganisms has become an issue of public concern, especially the indirect effect of plant metabolisms caused by the insertion of foreign genes. Methanogenesis, which is regarded as a critical ecological process in paddy soil, is influenced by plant root exudates; these are mainly derived from photosynthesis. The variations in root exudates across the Bt and Ck rice suggested the indirect influence of foreign gene insertion. DNA-SIP successfully traced the active methanogenic archaeal populations assimilating 13 C-labeled photosynthetic carbon and found a strong influence of planting Bt rice on active methanogens. As a consequence, we proposed that analysis of functionally active microorganisms is more suitable for

[Temperature sensitivity of CO2 fluxes from rhizosphere soil mineralization and root decomposition in Pinus massoniana and Castanopsis sclerophylla forests].

PubMed

Liu, Yu; Hu, Xiao-Fei; Chen, Fu-Sheng; Yuan, Ping-Cheng

2013-06-01

Rhizospheric and non-rhizospheric soils and the absorption, transition, and storage roots were sampled from the mid-subtropical Pinus massoniana and Castanopsis sclerophylla forests to study the CO2 fluxes from soil mineralization and root decomposition in the forests. The samples were incubated in closed jars at 15 degrees C, 25 degrees C, 35 degrees C, and 45 degrees C, respectively, and alkali absorption method was applied to measure the CO2 fluxes during 53 days incubation. For the two forests, the rhizospheric effect (ratio of rhizospheric to non-rhizospheric soil) on the CO2 flux from soil mineralization across all incubation temperature ranged from 1.12 to 3.09, with a decreasing trend along incubation days. There was no significant difference in the CO2 flux from soil mineralization between the two forests at 15 degrees C, but the CO2 flux was significantly higher in P. massoniana forest than in C. sclerophylla forest at 25 degrees C and 35 degrees C, and in an opposite pattern at 45 degrees C. At all incubation temperature, the CO2 release from the absorption root decomposition was higher than that from the transition and storage roots decomposition, and was smaller in P. massoniana than in C. sclerophylla forest for all the root functional types. The Q10 values of the CO2 fluxes from the two forests were higher for soils (1.21-1.83) than for roots (0.96-1.36). No significant differences were observed in the Q10 values of the CO2 flux from soil mineralization between the two forests, but the Q10 value of the CO2 flux from root decomposition was significantly higher in P. massoniana than in C. sclerophylla forest. It was suggested that the increment of CO2 flux from soil mineralization under global warming was far higher than that from root decomposition, and for P. massoniana than for C. sclerophylla forest. In subtropics of China, the adaptability of zonal climax community to global warming would be stronger than that of pioneer community.

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.

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

Speciation of arsenic in bulk and rhizosphere soils from artisanal cooperative mines in Bolivia.

PubMed

Acosta, Jose A; Arocena, Joselito M; Faz, Angel

2015-11-01

Soils near artisanal and small-scale gold mines (ASGM) have high arsenic (As) contents due to the presence of arsenopyrite in gold ores and accelerated accumulations due to mine wastes disposal practices and other mining activities. We determined the content and speciation to understand the fate and environmental risks of As accumulations in 24 bulk and 12 rhizosphere soil samples collected in the Virgen Del Rosario and the Rayo Rojo cooperative mines in the highlands of Bolivia. Mean total As contents in bulk and rhizosphere soils ranged from 13 to 64 mg kg(-1) and exceeded the soil environmental quality guidelines of Canada. Rhizosphere soils always contained at least twice the As contents in the bulk soil. Elemental mapping using 4×5 μm synchrotron-generated X-ray micro-beam revealed As accumulations in areas enriched with Fe. Results of As-X-ray Absorption Near Edge Spectroscopy (As-XANES) showed that only As(V) species was detectable in all samples regardless of As contents, size fractions and types of vegetation. Although the toxicity of As(V) is less than As(III), we suggest that As uptake of commonly-grazed vegetation by alpaca and llama must be determined to fully understand the environmental risks of high As in soils near ASGM in Bolivia. In addition, knowledge on the speciation of the As bio-accessible fraction will provide another useful information to better understand the fate and transfer of As from soils into the food chain in environments associated with the ASGM in Bolivia and other parts of the world. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-03-01

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

Distinct effects of struvite and biochar amendment on the class 1 integron antibiotic resistance gene cassettes in phyllosphere and rhizosphere.

PubMed

An, Xin-Li; Chen, Qing-Lin; Zhu, Dong; Su, Jian-Qiang

2018-08-01

Struvite recovered from wastewater is promising for recycling phosphorus into soil as fertilizers. However, struvite application may prompt the proliferation of antibiotic resistance in soil and plant. This study examined the impacts of struvite application and biochar amendment on integrons abundance and gene cassette contexts in rhizosphere soil and phyllosphere using quantitative PCR and clone library analysis. Microcosm experiments revealed that class 1 integron was the most prevalent in all samples, with higher concentration and higher relative abundance in rhizosphere than those in phyllosphere. The majority of resistance gene cassettes were associated with genes encoding resistance to aminoglycosides, beta-lactams and chloramphenicols. Struvite application significantly increased the genetic diversity of antibiotic resistance gene cassettes in both rhizosphere and phyllosphere. However, biochar amendment attenuated the increasing effect of struvite application exerting on the class 1 integron antibiotic resistance gene cassette pool in phyllosphere. These findings highlighted human activities to be the source of integron gene cassette pool and raised the possibility of using biochar amendment as an alternative mean for mitigating antibiotic resistance in environments. Copyright © 2018 Elsevier B.V. All rights reserved.

Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling

PubMed Central

Qin, Yuxuan; Shang, Qingmao; Zhang, Ying; Li, Pinglan; Chai, Yunrong

2017-01-01

Vegetable plug seedling has become the most important way to produce vegetable seedlings in China. This seedling method can significantly improve the quality and yield of vegetables compared to conventional methods. In the process of plug seedling, chemical fertilizers or pesticides are often used to improve the yield of the seedlings albeit with increasing concerns. Meanwhile, little is known about the impact of beneficial bacteria on the rhizosphere microbiota and the growth conditions of vegetables during plug seedling. In this study, we applied a culture-independent next-generation sequencing-based approach and investigated the impact of a plant beneficial bacterium, Bacillus amyloliquefaciens L-S60, on the composition and dynamics of rhizosphere microbiota and the growth conditions of cucumbers during plug seedling. Our results showed that application of L-S60 significantly altered the structure of the bacterial community associated with the cucumber seedling; presence of beneficial rhizosphere species such as Bacillus, Rhodanobacter, Paenibacillus, Pseudomonas, Nonomuraea, and Agrobacterium was higher upon L-S60 treatment than in the control group. We also measured the impact of L-S60 application on the physiological properties of the cucumber seedlings as well as the availability of main mineral elements in the seedling at different time points during the plug seedling. Results from those measurements indicated that L-S60 application promoted growth conditions of cucumber seedlings and that more available mineral elements were detected in the cucumber seedlings from the L-S60 treated group than from the control group. The findings in this study provided evidence for the beneficial effects of plant growth-promoting rhizosphere bacteria on the bacterial community composition and growth conditions of the vegetables during plug seedling. PMID:29312278

Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer.

PubMed

Coelho, Marcia Reed Rodrigues; de Vos, Marjon; Carneiro, Newton Portilho; Marriel, Ivanildo Evódio; Paiva, Edilson; Seldin, Lucy

2008-02-01

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). The nifH gene was amplified directly from DNA extracted from the rhizospheres, and the PCR products cloned and sequenced. Four clone libraries were generated from the nifH fragments and 245 sequences were obtained. Most of the clones (57%) were closely related to nifH genes of uncultured bacteria. NifH clones affiliated with Azohydromonas spp., Ideonella sp., Rhizobium etli and Bradyrhizobium sp. were found in all libraries. Sequences affiliated with Delftia tsuruhatensis were found in the rhizosphere of both cultivars sown with high levels of nitrogen, while clones affiliated with Methylocystis sp. were detected only in plants sown under low levels of nitrogen. Moreover, clones affiliated with Paenibacillus durus could be found in libraries from the cultivar IS 5322-C sown either in high or low amounts of fertilizer. This study showed that the amount of nitrogen used for fertilization is the overriding determinative factor that influenced the nitrogen-fixing community structures in sorghum rhizospheres cultivated in Cerrado soil.

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

PubMed

Ullah, Sami; Bano, Asghari

2015-04-01

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

Use of Endophytic and Rhizosphere Actinobacteria from Grapevine Plants To Reduce Nursery Fungal Graft Infections That Lead to Young Grapevine Decline

PubMed Central

Álvarez-Pérez, José Manuel; González-García, Sandra; Cobos, Rebeca; Olego, Miguel Ángel; Ibañez, Ana; Díez-Galán, Alba; Garzón-Jimeno, Enrique

2017-01-01

ABSTRACT Endophytic and rhizosphere actinobacteria isolated from the root system of 1-year-old grafted Vitis vinifera plants were evaluated for their activities against fungi that cause grapevine trunk diseases. A total of 58 endophytic and 94 rhizosphere isolates were tested. Based on an in vitro bioassay, 15.5% of the endophytic isolates and 30.8% of the rhizosphere isolates exhibited antifungal activity against the fungal pathogen Diplodia seriata, whereas 13.8% of the endophytic isolates and 16.0% of the rhizosphere isolates showed antifungal activity against Dactylonectria macrodidyma (formerly Ilyonectria macrodidyma). The strains which showed the greatest in vitro efficacy against both pathogens were further analyzed for their ability to inhibit the growth of Phaeomoniella chlamydospora and Phaeoacremonium minimum (formerly Phaeoacremonium aleophilum). Based on their antifungal activity, three rhizosphere isolates and three endophytic isolates were applied on grafts in an open-root field nursery in a 3-year trial. The field trial led to the identification of one endophytic strain, Streptomyces sp. VV/E1, and two rhizosphere isolates, Streptomyces sp. VV/R1 and Streptomyces sp. VV/R4, which significantly reduced the infection rates produced by the fungal pathogens Dactylonectria sp., Ilyonectria sp., P. chlamydospora, and P. minimum, all of which cause young grapevine decline. The VV/R1 and VV/R4 isolates also significantly reduced the mortality level of grafted plants in the nursery. This study shows that certain actinobacteria could represent a promising new tool for controlling fungal trunk pathogens that infect grapevine plants through the root system in nurseries. IMPORTANCE Grapevine trunk diseases are a major threat to the wine and grape industry worldwide. They cause a significant reduction in yields as well as in grape quality, and they can even cause plant death. Trunk diseases are caused by fungal pathogens that enter through pruning wounds and

Use of Endophytic and Rhizosphere Actinobacteria from Grapevine Plants To Reduce Nursery Fungal Graft Infections That Lead to Young Grapevine Decline.

PubMed

Álvarez-Pérez, José Manuel; González-García, Sandra; Cobos, Rebeca; Olego, Miguel Ángel; Ibañez, Ana; Díez-Galán, Alba; Garzón-Jimeno, Enrique; Coque, Juan José R

2017-12-15

Endophytic and rhizosphere actinobacteria isolated from the root system of 1-year-old grafted Vitis vinifera plants were evaluated for their activities against fungi that cause grapevine trunk diseases. A total of 58 endophytic and 94 rhizosphere isolates were tested. Based on an in vitro bioassay, 15.5% of the endophytic isolates and 30.8% of the rhizosphere isolates exhibited antifungal activity against the fungal pathogen Diplodia seriata , whereas 13.8% of the endophytic isolates and 16.0% of the rhizosphere isolates showed antifungal activity against Dactylonectria macrodidyma (formerly Ilyonectria macrodidyma ). The strains which showed the greatest in vitro efficacy against both pathogens were further analyzed for their ability to inhibit the growth of Phaeomoniella chlamydospora and Phaeoacremonium minimum (formerly Phaeoacremonium aleophilum ). Based on their antifungal activity, three rhizosphere isolates and three endophytic isolates were applied on grafts in an open-root field nursery in a 3-year trial. The field trial led to the identification of one endophytic strain, Streptomyces sp. VV/E1, and two rhizosphere isolates, Streptomyces sp. VV/R1 and Streptomyces sp. VV/R4, which significantly reduced the infection rates produced by the fungal pathogens Dactylonectria sp., Ilyonectria sp., P. chlamydospora , and P. minimum , all of which cause young grapevine decline. The VV/R1 and VV/R4 isolates also significantly reduced the mortality level of grafted plants in the nursery. This study shows that certain actinobacteria could represent a promising new tool for controlling fungal trunk pathogens that infect grapevine plants through the root system in nurseries. IMPORTANCE Grapevine trunk diseases are a major threat to the wine and grape industry worldwide. They cause a significant reduction in yields as well as in grape quality, and they can even cause plant death. Trunk diseases are caused by fungal pathogens that enter through pruning wounds and/or the

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

USDA-ARS?s Scientific Manuscript database

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...

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola) and characterization of osmoregulatory genes in halophilic Bacilli.

PubMed

Mukhtar, Salma; Mehnaz, Samina; Mirza, Muhammad Sajjad; Mirza, Babur Saeed; Malik, Kauser Abdulla

2018-04-27

Salinity is one of the major abiotic stresses, with a total of 3% of the world's land mass being affected by salinity. Approximately 6.3 million hectares of land in Pakistan is affected by salinity to varying degree and most of the areas are arid to semiarid with low annual precipitation. The aim of present study is to identify and characterize Bacillus and Bacillus-derived bacterial genera from the rhizospheric and non-rhizospheric soil samples from Khewra Salt Mine, Pakistan by using culture-independent as well as culture-dependent methods. Seven Bacillus-like bacterial genera Bacillus, Halobacillus, Virgibacillus, Brevibacillus, Paenibacillus, Tumebacillus and Lysinibacillus were detected by using pyrosequencing analysis whereas only four genera Bacillus, Halobacillus, Oceanobacillus and Virgibacillus were identified by culture-dependent methods. Most of Bacillus-like isolates identified in this study were moderately halophilic, alkaliphilic and mesophilic bacteria and were considered as a good source of hydrolytic enzymes because of their ability to degrade proteins, carbohydrates and lipids. Eight Bacillus-like strains from the genera Bacillus, Halobacillus, Oceanobacillus and Virgibacillus showed positive results for the presence of ectABC gene cluster (ectoine), six strains could synthesize betaine from choline and six strains tested positive for the synthesis of proline from either glutamate or ornithine by using proline dehydrogenase enzyme.

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

PubMed

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

2013-12-01

Beneficial plant-associated bacteria play a key role in supporting and/or promoting plant growth and health. Plant growth promoting bacteria present in the rhizosphere of crop plants can directly affect plant metabolism or modulate phytohormone production or degradation. We isolated 355 bacteria from the rhizosphere of rice plants grown in the farmers' fields in the coastal rice field soil from five different locations of the Ganjam district of Odisha, India. Six bacteria producing both ACC deaminase (ranging from 603.94 to 1350.02 nmol α-ketobutyrate mg(-1)  h(-1) ) and indole acetic acid (IAA; ranging from 10.54 to 37.65 μM ml(-1) ) in pure cultures were further identified using polyphasic taxonomy including BIOLOG((R)) , FAME analysis and the 16S rRNA gene sequencing. Phylogenetic analyses of the isolates resulted into five major clusters to include members of the genera Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Seed inoculation of rice (cv. Naveen) by the six individual PGPR isolates had a considerable impact on different growth parameters including root elongation that was positively correlated with ACC deaminase activity and IAA production. The cultures also had other plant growth attributes including ammonia production and at least two isolates produced siderophores. Study indicates that presence of diverse rhizobacteria with effective growth-promoting traits, in the rice rhizosphere, may be exploited for a sustainable crop management under field conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular and Imaging Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

NASA Astrophysics Data System (ADS)

Dohnalkova, A.; Tfaily, M.; Smith, A. P.; Chu, R. K.; Crump, A.; Brislawn, C.; Varga, T.; Shi, Z.; Thomashow, L. S.; Harsh, J. B.; Balogh-Brunstad, Z.; Keller, C. K.

2017-12-01

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is limited. The objective of this study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix. We hypothesized that nutrient limitation would cause formation of microbially-produced C constituents that would contribute to SOM stabilization. We focused on the processes of rhizodeposition in the rhizosphere, and we utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of the microbial community and the newly-formed SOM compounds in the rhizosphere and the bulk soil. We considered implications regarding their degree of long-term stability. The microbes in this controlled, nutrient-limited system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. These findings provide insight into the various degrees of stability of microbial SOM products in ecosystems and evidence that the residual biogenic material associated with mineral matrices may be important components in current carbon cycle models.

Diversity of rhizosphere soil arbuscular mycorrhizal fungi in various soybean cultivars under different continuous cropping regimes.

PubMed

Jie, Weiguang; Liu, Xiaorui; Cai, Baiyan

2013-01-01

Recent studies have shown that continuous cropping in soybean causes substantial changes to the microbial community in rhizosphere soil. In this study, we investigated the effects of continuous cropping for various time periods on the diversity of rhizosphere soil arbuscular mycorrhizal (AM) fungi in various soybean cultivars at the branching stage. The soybean cultivars Heinong 37 (an intermediate cultivar), Heinong 44 (a high-fat cultivar) and Heinong 48 (a high-protein cultivar) were seeded in a field and continuously cropped for two or three years. We analyzed the diversity of rhizosphere soil AM fungi of these soybean plants at the branching stage using morphological and denaturing gradient gel electrophoresis (DGGE) techniques. The clustering analysis of unweighted pair-group method with arithmetic averages (UPGMA) was then used to investigate the AM fungal community shifts. The results showed that increasing the number of years of continuous cropping can improve the colonization rate of AM fungi in different soybean cultivars at the branching stage. The dominant AM fungi in the experimental fields were Funneliformismosseae and Glomus spp. The number of years of continuous cropping and the soybean cultivar both had obvious effects on the diversity of AM fungi, which was consistent with the results of colonization rate analysis. This study establishes a basis for screening dominant AM fungi of soybean. In addition, the results of this study may be useful for the development of AM fungal inoculants.

Diversity of Rhizosphere Soil Arbuscular Mycorrhizal Fungi in Various Soybean Cultivars under Different Continuous Cropping Regimes

PubMed Central

Jie, Weiguang; Liu, Xiaorui; Cai, Baiyan

2013-01-01

Recent studies have shown that continuous cropping in soybean causes substantial changes to the microbial community in rhizosphere soil. In this study, we investigated the effects of continuous cropping for various time periods on the diversity of rhizosphere soil arbuscular mycorrhizal (AM) fungi in various soybean cultivars at the branching stage. The soybean cultivars Heinong 37 (an intermediate cultivar), Heinong 44 (a high-fat cultivar) and Heinong 48 (a high-protein cultivar) were seeded in a field and continuously cropped for two or three years. We analyzed the diversity of rhizosphere soil AM fungi of these soybean plants at the branching stage using morphological and denaturing gradient gel electrophoresis (DGGE) techniques. The clustering analysis of unweighted pair-group method with arithmetic averages (UPGMA) was then used to investigate the AM fungal community shifts. The results showed that increasing the number of years of continuous cropping can improve the colonization rate of AM fungi in different soybean cultivars at the branching stage. The dominant AM fungi in the experimental fields were Funneliformismosseae and Glomus spp. The number of years of continuous cropping and the soybean cultivar both had obvious effects on the diversity of AM fungi, which was consistent with the results of colonization rate analysis. This study establishes a basis for screening dominant AM fungi of soybean. In addition, the results of this study may be useful for the development of AM fungal inoculants. PMID:23977368

Effects of tillage technologies and application of biopreparations on micromycetes in the rhizosphere and rhizoplane of spring wheat

NASA Astrophysics Data System (ADS)

Shirokikh, I. G.; Kozlova, L. M.; Shirokikh, A. A.; Popov, F. A.; Tovstik, E. V.

2017-07-01

The population density and structure of complexes of soil microscopic fungi in the rhizosphere and rhizoplane of spring wheat ( Triticum aestivum L.), plant damage by root rot and leaf diseases, and crop yield were determined in a stationary field experiment on a silty loamy soddy-podzolic soil (Albic Retisol (Loamic, Aric)) in dependence on the soil tillage technique: (a) moldboard plowing to 20-22 cm and (b) non-inversive tillage to 14-16 cm. The results were treated with the two-way ANOVA method. It was shown that the number of fungal propagules in the rhizosphere and rhizoplane of plants in the variant with non-inversive tillage was significantly smaller than that in the variant with plowing. Minimization of the impact on the soil during five years led to insignificant changes in the structure of micromycete complexes in the rhizosphere of wheat. The damage of the plants with root rot and leaf diseases upon non-inversive tillage did not increase in comparison with that upon plowing. Wheat yield in the variant with non-inversive tillage was insignificantly lower than that in the variant with moldboard plowing. The application of biopreparations based on the Streptomyces hygroscopicus A4 and Pseudomonas aureofaciens BS 1393 resulted in a significant decrease of plant damage with leaf rust.

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers.

PubMed

Allard, Sarah M; Walsh, Christopher S; Wallis, Anna E; Ottesen, Andrea R; Brown, Eric W; Micallef, Shirley A

2016-12-15

Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. 'BHN602' grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM (R=0.87, p=0.001 in year 1; R=0.93, p=0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil (p<0.05) across the field and corresponding shifts in water activity were positively (R 2 =0.52, p=0.005) and negatively (R 2 =0.48, p=0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Microbial cooperation in the rhizosphere improves liquorice growth under salt stress

PubMed Central

Egamberdieva, Dilfuza; Wirth, Stephan; Li, Li; Abd-Allah, Elsayed Fathi

2017-01-01

ABSTRACT 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. PMID:27780398

Effectiveness of Nitrification Inhibition on Various Species of Brachiaria Grass Rhizosphere

NASA Astrophysics Data System (ADS)

Purwanto; Supriyadi; Hindrayani, Aniek

2018-02-01

Nitrification has the potential to decrease the efficiency of nitrogen utilization by plants. The use of nitrifying inhibitory chemicals proved to be effective in controlling nitrification, but also affects beneficial soil microbes. Another attempt to inhibit the more environmentally-friendly nitrification is to use plants that have allelochemical nitrification inhibiting compounds such as the grasses of Brachiaria. The aim of this research is to know the effectivity of B.mutica, B.decumbens, and B.humidicola as inhibitors of nitrification rate in soil. The experiment was carried out by pot experimental method based on nondestructive sampling and Complete Randomized Design, consisting of Brachiaria plant types and various doses of N fertilizer, 100 kg/ha, 150 kg/ha, 200 kg/ha. The results of this study show that 1) B.mutica, B.decumbens, and B.humidicola, highly significant to the soil potential nitrification, but the treatment of various doses of N fertilizer is not significant to the soil potential nitrification. 2) the highest soil potential nitrification in B.mutica rhizosphere was 5.160 mg NO2-/g of soil/5h, while the lowest soil potential nitrification in the rhizosphere of B.humidicola plant was 0.414 mg NO2-/g/5h. 3) From the four treatment of Brachiaria plants can be concluded B.humidicola plant more effective in inhibition of nitrification.

Impact of phenazine-1-carboxylic acid upon iron speciation and microbial biomass in the rhizosphere of wheat

NASA Astrophysics Data System (ADS)

LeTourneau, M.; Marshall, M.; Grant, M.; Freeze, P.; Cliff, J. B.; Lai, B.; Strawn, D. G.; Thomashow, L. S.; Weller, D. M.; Harsh, J. B.

2015-12-01

Phenazine-1-carboxylic acid (PCA) is a redox-active antibiotic produced by diverse bacterial taxa, and has been shown to facilitate interactions between biofilms and iron (hydr)oxides in culture systems (Wang et al. 2011, J Bacteriol 192: 365). Because rhizobacterial biofilms are a major sink for plant-derived carbon and source for soil organic matter (SOM), and Fe (hydr)oxides have reactive surfaces that influence the stability of microbial biomass and SOM, PCA-producing rhizobacteria could influence soil carbon fluxes. Large populations of Pseudomonas fluorescens strains producing PCA in concentrations up to 1 μg/g root have been observed in the rhizosphere of non-irrigated wheat fields covering 1.56 million hectares of central Washington state. This is one of the highest concentrations ever reported for a natural antibiotic in a terrestrial ecosystem (Mavrodi et al. 2012, Appl Environ Microb 78: 804). Microscopic comparisons of PCA-producing (PCA+) and non-PCA-producing (PCA-) rhizobacterial colony morphologies, and comparisons of Fe extractions from rhizosphere soil inoculated with PCA+ and PCA- strains suggest that PCA promotes biofilm development as well as dramatic Fe transformations throughout the rhizosphere (unpublished data). In order to illustrate PCA-mediated interactions between biofilms and Fe (hydr)oxides in the rhizosphere, identify the specific Fe phases favored by PCA, and establish the ramifications for stability and distribution of microbial biomass and SOM, we have collected electron micrographs, X-ray fluorescence images, X-ray absorption near-edge spectra, and secondary-ion mass spectrometry images of wheat root sections inoculated with 15N-labelled PCA+ or PCA- rhizobacteria. These images and spectra allow us to assess the accumulation, turnover, and distribution of microbial biomass, the associations between Fe and other nutrients such as phosphorus, and the redox status and speciation of iron in the presence and absence of PCA. This

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

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

PubMed

Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

2016-01-15

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and

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.

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

USDA-ARS?s Scientific Manuscript database

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...

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems

USDA-ARS?s Scientific Manuscript database

Field experiments were conducted to evaluate the effects of soil solarization or cover cropping on bell pepper (Capsicum annuum) and lima bean (Phaseolus lunatus, L.) rhizosphere microorganisms. In Experiment I, flat surface solarization (FSS), raised bed solarization (RBS), cowpea (Vigna unguiculat...

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.

Effect of Arbuscular Mycorrhizal Fungi on Plant Biomass and the Rhizosphere Microbial Community Structure of Mesquite Grown in Acidic Lead/Zinc Mine Tailings

PubMed Central

Solís-Domínguez, Fernando A.; Valentín-Vargas, Alexis; Chorover, Jon; Maier, Raina M.

2011-01-01

Mine tailings in arid and semi-arid environments are barren of vegetation and subject to eolian dispersion and water erosion. Revegetation is a cost-effective strategy to reduce erosion processes and has wide public acceptance. A major cost of revegetation is the addition of amendments, such as compost, to allow plant establishment. In this paper we explore whether arbuscular mycorrhizal fungi (AMF) can help support plant growth in tailings at a reduced compost concentration. A greenhouse experiment was performed to determine the effects of three AMF inocula on biomass, shoot accumulation of heavy metals, and changes in the rhizosphere microbial community structure of the native plant Prosopis juliflora (mesquite). Plants were grown in an acidic lead/zinc mine tailings amended with 10% (w/w) compost amendment, which is slightly sub-optimal for plant growth in these tailings. After two months, AMF-inoculated plants showed increased dry biomass and root length (p < 0.05) and effective AMF colonization compared to controls grown in uninoculated compost-amended tailings. Mesquite shoot tissue lead and zinc concentrations did not exceed domestic animal toxicity limits regardless of whether AMF inoculation was used. The rhizosphere microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) profiles of the small subunit RNA gene for bacteria and fungi. Canonical correspondence analysis (CCA) of DGGE profiles showed that the rhizosphere fungal community structure at the end of the experiment was significantly different from the community structure in the tailings, compost, and AMF inocula prior to planting. Further, CCA showed that AMF inoculation significantly influenced the development of both the fungal and bacterial rhizosphere community structures after two months. The changes observed in the rhizosphere microbial community structure may be either a direct effect of the AMF inocula, caused by changes in plant physiology induced by

Carbon transfer from plant roots to soil - NanoSIMS analyses of undisturbed rhizosphere samples

NASA Astrophysics Data System (ADS)

Vidal, Alix; Hirte, Juliane; Bender, S. Franz; Mayer, Jochen; Gattinger, Andreas; Mueller, Carsten W.

2017-04-01

Soils are composed of a wide diversity of organic and mineral compounds, interacting to form complex mosaics of microenvironments. Roots and microorganisms are both key sources of organic carbon (OC). The volume of soil around living roots, i.e. the rhizosphere, is a privileged area for soil microbial activity and diversity. The microscopic observation of embedded soil sections has been applied since the 1950´s and has enabled observation of the rhizosphere at the smallest scale of organism interaction, i.e. at the level of root cells and bacteria (Alexander and Jackson, 1954). However, the observation of microorganisms in their intact environment, especially in soil, remains challenging. Existing microscopic images do not provide clear evidence of the chemical composition of compounds observed in the rhizosphere. Nano-scale secondary ion mass spectrometry (NanoSIMS) is a high spatial resolution method providing elemental and isotopic maps of organic and mineral materials. This technic has been increasingly used in soil science during the last decade (Hermann et al., 2007; Vogel et al., 2014) and more specifically for undisturbed soil sample observations (Vidal et al., 2016). In the present study, NanoSIMS was used to illustrate the biological, physical and chemical processes occurring in the rhizosphere at the microscale. To meet this objective, undisturbed rhizosphere samples were collected from a field experiment in Switzerland where wheat plants were pulse-labelled with 99% 13C-CO2 in weekly intervals throughout the growing season and sampled at flowering. Samples were embedded, sectioned, polished and analyzed with NanoSIMS, obtaining secondary ion images of 12C, 13C, 12C14N, 16O, 31P16O2, and 32S. The δ13C maps were obtained thanks to 12C and 13C images. 13C labelled root cells were clearly distinguished on images and presented highly variable δ13C values. Labelled spots (< 1 µm), identified as bacteria, were located at the root cell surroundings. These

Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil

PubMed Central

Caldwell, Adam Collins; Silva, Lívia Carneiro Fidéles; da Silva, Cynthia Canêdo; Ouverney, Cleber Costa

2015-01-01

Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 coffee plant rhizospheres (soil directly influenced by the plant root exudates) and 10 control sites (soil 5 m away from the coffee plantation) at each of the three farms for a total of 90 samples. Profiling of 16S rRNA gene V4 regions revealed high levels of prokaryotic diversity in all three farms, with thousands of species level operational taxonomic units identified in each farm. Additionally, a statistically significant difference was found between each farm’s coffee rhizosphere microbiome, as well as between coffee rhizosphere soils and control soils. Two groups of prokaryotes associated with the nitrogen cycle, the archaeal genus Candidatus Nitrososphaera and the bacterial order Rhizobiales were found to be abundant and statistically different in composition between the three farms and in inverse relationship to each other. Many of the nitrogen-fixing genera known to enhance plant growth were found in low numbers (e.g. Rhizobium, Agrobacter, Acetobacter, Rhodospirillum, Azospirillum), but the families in which they belong had some of the highest relative abundance in the dataset, suggesting many new groups may exist in these samples that can be further studied as potential plant growth-promoting bacteria to improve coffee production while diminishing negative

Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil.

PubMed

Caldwell, Adam Collins; Silva, Lívia Carneiro Fidéles; da Silva, Cynthia Canêdo; Ouverney, Cleber Costa

2015-01-01

Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 coffee plant rhizospheres (soil directly influenced by the plant root exudates) and 10 control sites (soil 5 m away from the coffee plantation) at each of the three farms for a total of 90 samples. Profiling of 16S rRNA gene V4 regions revealed high levels of prokaryotic diversity in all three farms, with thousands of species level operational taxonomic units identified in each farm. Additionally, a statistically significant difference was found between each farm's coffee rhizosphere microbiome, as well as between coffee rhizosphere soils and control soils. Two groups of prokaryotes associated with the nitrogen cycle, the archaeal genus Candidatus Nitrososphaera and the bacterial order Rhizobiales were found to be abundant and statistically different in composition between the three farms and in inverse relationship to each other. Many of the nitrogen-fixing genera known to enhance plant growth were found in low numbers (e.g. Rhizobium, Agrobacter, Acetobacter, Rhodospirillum, Azospirillum), but the families in which they belong had some of the highest relative abundance in the dataset, suggesting many new groups may exist in these samples that can be further studied as potential plant growth-promoting bacteria to improve coffee production while diminishing negative

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.

Remediation aspect of microbial changes of plant rhizosphere in mercury contaminated soil.

PubMed

Sas-Nowosielska, Aleksandra; Galimska-Stypa, Regina; Kucharski, Rafał; Zielonka, Urszula; Małkowski, Eugeniusz; Gray, Laymon

2008-02-01

Phytoremediation, an approach that uses plants to remediate contaminated soil through degradation, stabilization or accumulation, may provide an efficient solution to some mercury contamination problems. This paper presents growth chamber experiments that tested the ability of plant species to stabilize mercury in soil. Several indigenous herbaceous species and Salix viminalis were grown in soil collected from a mercury-contaminated site in southern Poland. The uptake and distribution of mercury by these plants were investigated, and the growth and vitality of the plants through a part of one vegetative cycle were assessed. The highest concentrations of mercury were found at the roots, but translocation to the aerial part also occurred. Most of the plant species tested displayed good growth on mercury contaminated soil and sustained a rich microbial population in the rhizosphere. The microbial populations of root-free soil and rhizosphere soil from all species were also examined. An inverse correlation between the number of sulfur amino acid decomposing bacteria and root mercury content was observed. These results indicate the potential for using some species of plants to treat mercury contaminated soil through stabilization rather than extraction. The present investigation proposes a practical cost-effective temporary solution for phytostabilization of soil with moderate mercury contamination as well as the basis for plant selection.

Biochar reduces the bioaccumulation of PAHs from soil to carrot (Daucus carota L.) in the rhizosphere: A mechanism study.

PubMed

Ni, Ni; Song, Yang; Shi, Renyong; Liu, Zongtang; Bian, Yongrong; Wang, Fang; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-12-01

The aim of this study was to reveal the mechanisms on how biochar reduces bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) in tuberous vegetables. Corn straw-derived biochar pyrolyzed at 300°C (CB300) or bamboo-derived biochar pyrolyzed at 700°C (BB700) was amended into PAH-contaminated soil planted with carrot (Daucus carota L.). After 150days, 2% CB300 or 2% BB700 amendments significantly reduced the bioaccumulation of PAHs in carrot root (p<0.05), especially for high-molecular-weight PAHs. In the non-rhizosphere, either CB300 or BB700 suppressed PAH dissipation and decreased the bioavailability via adsorption processes. Compared to the control, the total concentration of PAHs in the rhizosphere was higher in the 2% BB700 treatment but the bioavailable concentration was lower. This indicates that BB700 decreased the bioavailability of PAHs primarily via immobilization (adsorption processes). By contrast, the total and bioavailable PAH concentrations were both lower in the 2% CB300 treatment than those in the control. The abundance of bacteria such as Arthrobacter and Flavobacterium and the total number of genes playing important roles in microbial PAH degradation processes increased significantly (p<0.05), which were likely responsible for the rapid dissipation of PAHs in the 2% CB300 treatment in the rhizosphere. These results indicate that CB300 decreased the PAH bioavailability primarily via increasing degradation of PAHs by indigenous microorganisms. The two biochars both showed better effectiveness at reducing the bioavailability of high-molecular-weight PAHs than the low-molecular-weight PAHs in the rhizosphere. Therefore, the mechanisms on how biochar reduces the PAH uptake into carrot are dependent on the type of biochar (e.g., pyrolysis temperature and feedstock) and root presence. Copyright © 2017 Elsevier B.V. All rights reserved.

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 ...

Isolation and Characterization of a Phosphorus-Solubilizing Bacterium from Rhizosphere Soils and Its Colonization of Chinese Cabbage (Brassica campestris ssp. chinensis)

PubMed Central

Wang, Zhen; Xu, Guoyi; Ma, Pengda; Lin, Yanbing; Yang, Xiangna; Cao, Cuiling

2017-01-01

Phosphate-solubilizing bacteria (PSB) can promote the dissolution of insoluble phosphorus (P) in soil, enhancing the availability of soluble P. Thus, their application can reduce the consumption of fertilizer and aid in sustainable agricultural development. From the rhizosphere of Chinese cabbage plants grown in Yangling, we isolated a strain of PSB (YL6) with a strong ability to dissolve P and showed that this strain promoted the growth of these plants under field conditions. However, systematic research on the colonization of bacteria in the plant rhizosphere remains deficient. Thus, to further study the effects of PSB on plant growth, in this study, green fluorescent protein (GFP) was used to study the colonization of YL6 on Chinese cabbage roots. GFP expression had little effect on the ability of YL6 to grow and solubilize P. In addition, the GFP-expressing strain stably colonized the Chinese cabbage rhizosphere (the number of colonizing bacteria in the rhizosphere soil was 4.9 lg CFU/g). Using fluorescence microscopy, we observed a high abundance of YL6-GFP bacteria at the Chinese cabbage root cap and meristematic zone, as well as in the root hairs and hypocotyl epidermal cells. High quantities of GFP-expressing bacteria were recovered from Chinese cabbage plants during different planting periods for further observation, indicating that YL6-GFP had the ability to endogenously colonize the plants. This study has laid a solid and significant foundation for further research on how PSB affects the physiological processes in Chinese cabbage to promote plant growth. PMID:28798725

[Effect of Water Extracts from Rhizosphere Soil of Cultivated Astragalus membranaceus var. mongholicus on It's Seed Germination and Physiological Characteristics].

PubMed

Lang, Duo-yong; Fu, Xue-yan; Rong, Jia-wang; Zhang, Xin-hui

2015-01-01

To explore the relationship between continuous cropping obstacle and autotoxicity of Astragalus membranaceus var. mongholicus. Distilled water(CK), water extracts of rhizosphere soil(50, 100, 200 and 400 mg/mL) were applied to test their effect on early growth and physiological characteristics of Astragalus membranaceus var. mongholicus. The water extracts from rhizospher soil of cultivated Astragalus membranaceus var. mongholicus significantly increased seedling emergence rate, root length and vigor index of Astragalus membranaceus var. mongholicus seedling when at the concentration of 100 mg/mL or below, however,there was no significant effect at 200 mg/mL or higher. The water extracts from rhizosphere soil of cultivated Astragalus membranaceus var. mongholicus significantly reduced the SOD activity in Astragalus membranaceus var. mongholicus seedling at 400 mg/mL and POD activity at 200 mg/mL and 400 mg/mL,while significantly increased the MDA content. Water extracts from Astragalus membranaceus var. mongholicus rhizosphere soil significantly affected Astragalus membranaceus var. mongholicus germination and seedling growth in a concentration-dependent manner, generally, low concentrations increased the SOD and POD activity which improved seed germination and seedling growth, while high concentrations caused cell membrane damage of the seedling.

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

PubMed Central

Bell, Terrence H; El-Din Hassan, Saad; Lauron-Moreau, Aurélien; Al-Otaibi, Fahad; Hijri, Mohamed; Yergeau, Etienne; St-Arnaud, Marc

2014-01-01

Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray–Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg−1 hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities. PMID:23985744

The Competitiveness of Pseudomonas chlororaphis Carrying pJP4 Is Reduced in the Arabidopsis thaliana Rhizosphere

PubMed Central

Schmidt-Eisenlohr, Heike; Baron, Christian

2003-01-01

The effect of the large catabolic IncP plasmid pJP4 on the competitiveness of Pseudomonas chlororaphis SPR044 and on its derivatives SPR244 (GacS deficient), SPR344 (phenazine-1-carboxamide overproducer), and SPR644 (phenazine-1-carboxamide deficient) in the Arabidopsis thaliana rhizosphere was assessed. Solitary rhizosphere colonization by the wild type, SPR244, and SPR644 was not affected by the plasmid. The size of the population of SPR344 carrying pJP4, however, was significantly reduced compared to the size of the population of the plasmid-free derivative. The abiotic stress caused by phenazine-1-carboxamide overproduction probably resulted in a selective disadvantage for cells carrying pJP4. Next, the effect of biotic stress caused by coinoculation of other bacteria was analyzed. Cells carrying pJP4 had a selective disadvantage compared to plasmid-free cells in the presence of the efficient colonizer Pseudomonas fluorescens WCS417r. This effect was not observed after coinoculation with a variety of other bacteria, and it was independent of quorum sensing and phenazine-1-carboxamide production. Thus, the presence of large catabolic plasmids imposes a detectable metabolic burden in the presence of biotic stress. Plasmid transfer in the A. thaliana rhizosphere from P. chlororaphis and its derivatives to Ralstonia eutropha was determined by using culture-dependent and culture-independent techniques. With the cultivation-independent technique we detected a significantly higher portion of exconjugants, but pJP4 transfer was independent of the quorum-sensing system and of phenazine-1-carboxamide production. PMID:12620876

Water regime influences bulk soil and Rhizosphere of Cereus jamacaru bacterial communities in the Brazilian Caatinga biome.

PubMed

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

2013-01-01

We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes.

Water Regime Influences Bulk Soil and Rhizosphere of Cereus jamacaru Bacterial Communities in the Brazilian Caatinga Biome

PubMed Central

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

2013-01-01

We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes. PMID:24069212

[Effects of different crop rotations on growth of continuous cropping sorghum and its rhizosphere soil micro-environment.

PubMed

Wang, Jin Song; Fan, Fang Fang; Guo, Jun; Wu, Ai Lian; Dong, Er Wei; Bai, Wen Bin; Jiao, Xiao Yan

2016-07-01

The effects of crop rotation on sorghum [Sorghum biocolor (L) Moench] growth, rhizosphere microbial community and the activity of soil enzymes for successive crops of sorghum were evaluated. Five years of continuous monoculture sorghum as the control (CK) was compared to alfalfa and scallion planted in the fourth year. The results showed that incorporation of alfalfa and scallion into the rotation significantly improved sorghum shoot growth. Specifically, sorghum grain yield increased by 16.5% in the alfalfa rotation plots compared to the CK. The rotations also increased sorghum root system growth, with alfalfa or scallion rotation increasing sorghum total root length by 0.3 and 0.4 times, total root surface area by 0.6 and 0.5 times, root volume by 1.2 and 0.6 times, and root biomass by 1.0 and 0.3 times, respectively. Alfalfa rotation also expanded sorghum root distribution below the 10 cm soil depth. A Biolog analysis on biome functions in the sorghum flowering period indicated significantly higher microbial activity in the rotation plots. The alfalfa and scallion rotation increased the Shannon index by 0.2 and 0.1 times compared to the CK, and improved the sucrose activity in the rhizosphere soil. It was concluded that including alfalfa in rotation with sorghum improved sorghum rhizosphere soil environment, enhanced soil microbial enzyme activity, alleviated the obstacle of continuous cropping and thus increased the sorghum yield.

Transfer kinetics of phosphorus (P) in macrophyte rhizosphere and phytoremoval performance for lake sediments using DGT technique.

PubMed

Wu, Zhihao; Wang, Shengrui; Luo, Jun

2018-05-15

DGT (diffusive gradients in thin films) technique and DIFS (DGT induced fluxes in sediment) model are firstly designed for macrophyte-rhizobox system and in-situ macrophytes in Lake Erhai. Dynamics of phosphorus (P) transfer in Zizania latifolia (ZL) and Myriophyllum verticiilatur (MV) rhizosphere is revealed and phytoremediation performance for P in sediment is evaluated. Dynamic transfer process of P at DGT/sediment interface includes (i) diffusion flux and concentration gradients at DGT(root)/porewater interface leading to porewater concentration (C 0 ) depletion and (ii) P desorption from labile P pool in sediment solid to resupply C 0 depletion. Fe-redox controlled P release from Fe-bound P (BD-P2) and then NH 4 Cl-P1 in rhizosphere sediment resupplies porewater depletion due to DGT (root) sink. K d (labile P pool size in solid phase), r (resupply ratio) and kinetic exchange (Tc and k -1 ) lead to change characters of DIFS curves of (1) r against deployment time and (2) C solu (dissolved concentration) against distance at 24 h. They include two opposite types of "fast" and "slow" rate of resupplies. Sediment properties and DIFS parameters control P diffusion and resupply in rhizosphere sediment. Phytoremoval ability for sediment P in lake is estimated to be 23.4 (ZL) or 15.0 t a -1 (MV) by "DGT-flux" method. Copyright © 2018 Elsevier B.V. All rights reserved.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

PubMed

van Wyk, Deidré A B; Adeleke, Rasheed; Rhode, Owen H J; Bezuidenhout, Carlos C; Mienie, Charlotte

2017-09-01

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Plant community richness mediates inhibitory interactions and resource competition between Streptomyces and Fusarium populations in the rhizosphere

USDA-ARS?s Scientific Manuscript database

Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this w...

Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil.

PubMed

Priha; Grayston; Pennanen; Smolander

1999-10-01

The aim of this study was to determine whether Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) Karst.) and silver birch (Betula pendula Roth) seedlings have a selective influence on the soil microbial community structure and activity and whether this varies in different soils. Seedlings of pine, spruce and birch were planted into pots of two soil types: an organic soil and a mineral soil. Pots without seedlings were also included. After one growing season, microbial biomass C (C(mic)) and N (N(mic)), C mineralization, net ammonification, net nitrification, denitrification potential, phospholipid fatty acid (PLFA) patterns and community level physiological profiles (CLPPs) were measured in the rhizosphere soil of the seedlings. In the organic soil, C(mic) and N(mic) were higher in the birch rhizosphere than in pine and spruce rhizosphere. The C mineralization rate was not affected by tree species. Unplanted soil contained the highest amount of mineral N and birch rhizosphere the lowest, but rates of net N mineralization and net nitrification did not differ between treatments. The microbial community structure, measured by PLFAs, had changed in the rhizospheres of all tree species compared to the unplanted soil. Birch rhizosphere was most clearly separated from the others. There was more of the fungal specific fatty acid 18:2omega6,9 and more branched fatty acids, common in Gram-positive bacteria, in this soil. CLPPs, done with Biolog GN plates and 30 additional substrates, separated only birch rhizosphere from the others. In the mineral soil, roots of all tree species stimulated C mineralization in soil and prevented nitrification, but did not affect C(mic) and N(mic), PLFA patterns or CLPPs. The effects of different tree species did not vary in the mineral soil. Thus, in the mineral soil, the strongest effect on soil microbes was the presence of a plant, regardless of the tree species, but in the organic soil, different tree species varied in

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

Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities

PubMed Central

Khan, Mohammad S.; Sadat, Syed U.; Jan, Asad; Munir, Iqbal

2017-01-01

Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN) and Abasyne-95 (AB-95). However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S–23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal) between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters. PMID:28791039

Comparing WHAM 6 and MINEQL+ 4.5 for the chemical speciation of Cu2+ in the rhizosphere of forest soils.

PubMed

Cloutier-Hurteau, Benoît; Sauvé, Sébastien; Courchesne, François

2007-12-01

Metal speciation data calculated by modeling could give useful information regarding the fate of metals in the rhizospheric environment. However, no comparative study has evaluated the relative accuracy of speciation models in this microenvironment. Consequently, the present study evaluates the reliability of free Cu ion (Cu2+) activity modeled by WHAM 6 and MINEQL+ 4.5 for 18 bulk and 18 rhizospheric soil samples collected in two Canadian forested areas located near industrial facilities. The modeling of Cu speciation was performed on water extracts using pH, dissolved organic carbon (DOC), major ions, and total dissolved Al, Ca, Cu, Mg, and Zn concentrations as input data. Four scenarios representing the composition of dissolved organic substances using fulvic, humic, and acetic acids were derived from the literature and used in the modeling exercise. Different scenarios were used to contrast soil components (rhizosphere vs bulk) and soil pH levels (acidic vs neutral to alkaline). Reference Cu2+ activity values measured by an ion-selective electrode varied between 0.39 and 41 nM. The model MINEQL+ 4.5 provided good predictions of Cu2+ activities [root-mean-square residual (RMSR)= 0.37], while predictions from WHAM 6 were poor (RMSR = 1.74) because they overestimated Cu complexation with DOC. Modeling with WHAM 6 could be improved by adjusting the proportion of inert DOC and the composition of DOC (RMSR = 0.94), but it remained weaker than predictions with MINEQL+ 4.5. These results suggested that the discrepancies between speciation models were attributed to differences in the binding capacity of humic substances with Cu, where WHAM 6 appeared to be too aggressive. Therefore, we concluded that chemical interactions occurring between Cu and DOC were key factors for an accurate simulation of Cu speciation, especially in rhizospheric forest soils, where high variation of the DOC concentration and composition are observed.

Dissipation of phenanthrene and pyrene at the aerobic-anaerobic soil interface: differentiation induced by the rhizosphere of PAH-tolerant and PAH-sensitive rice (Oryza sativa L.) cultivars.

PubMed

He, Yan; Xia, Wen; Li, Xinfeng; Lin, Jiajiang; Wu, Jianjun; Xu, Jianming

2015-03-01

A pot experiment was conducted to reveal the removal of two polycyclic aromatic hydrocarbons (PAHs) (phenanthrene, PHE, and pyrene, PYR) during rice cultivation in a paddy field. The rhizosphere effect on facilitating dissipation of PAHs varied simultaneously as a function of soil properties, PAH types, cultivation time, and genotypes within rice cultivars, with differences performed for PYR but not PHE. Changes in soil PLFA profiles evidenced that the growth of rice roots modified the dominant species within rhizosphere microbial communities and induced a selective enrichment of Gram-negative aerobic bacteria capable of degrading, thereby resulting in the differentiated dissipation of PYR. While the insignificant differences in PHE dissipation might be attributed to its higher solubility and availability under flooded condition that concealed the differences in improvement of bioavailability for microorganisms between rhizosphere and non-rhizosphere, and between both soils and both rice cultivars. Our findings illustrate that the removal of PAHs in paddy soils was more complex relative to those in dryland soils. This was possibly due to the specialty of rice roots for oxygen secretion that provides development of redox heterogeneous microbial habitats at root-soil interface under flooded condition.

Respiration-to-DNA ratio reflects physiological state of microorganisms in root-free and rhizosphere soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, E.; Blagodatsky, S.; Kuzyakov, Y.

2009-04-01

The double-stranded DNA (dsDNA) content in soil can serve as a measure of microbial biomass under near steady-state conditions and quantitatively reflect the exponential microbial growth initiated by substrate addition. The yield of respired CO2 per microbial biomass unit (expressed as DNA content) could be a valuable physiological indicator reflecting state of soil microbial community. Therefore, investigations combining both analyses of DNA content and respiration of soil microorganisms under steady-state and during periods of rapid growth are needed. We studied the relationship between CO2 evolution and microbial dsDNA content in native and glucose-amended samples of root-free and rhizosphere soil under Beta vulgaris (Cambisol, loamy sand from the field experiment of the Institute of Agroecology FAL, Braunschweig, Germany). Quantity of dsDNA was determined by direct DNA isolation from soil with mechanic and enzymatic disruption of microbial cell walls with following spectrofluorimetric detection with PicoGreen (Blagodatskaya et al., 2003). Microbial biomass and the kinetic parameters of microbial growth were estimated by dynamics of the CO2 emission from soil amended with glucose and nutrients (Blagodatsky et al., 2000). The CO2 production rate was measured hourly at 22оС using an automated infrared-gas analyzer system. The overall increase in microbial biomass, DNA content, maximal specific growth rate and therefore, in the fraction of microorganisms with r-strategy were observed in rhizosphere as compared to bulk soil. The rhizosphere effect for microbial respiration, biomass and specific growth rate was more pronounced for plots with half-rate of N fertilizer compared to full N addition. The DNA content was significantly lower in bulk compared to rhizosphere soil both before and during microbial growth initiated by glucose amendment. Addition of glucose to the soil strongly increased the amount of CO2 respired per DNA unit. Without substrate addition the

Enhanced rhizosphere colonization of beneficial Bacillus amyloliquefaciens SQR9 by pathogen infection.

PubMed

Liu, Yunpeng; Zhang, Nan; Qiu, Meihua; Feng, Haichao; Vivanco, Jorge M; Shen, Qirong; Zhang, Ruifu

2014-04-01

Root exudates play important roles in root-soil microorganism interactions and can mediate tripartite interactions of beneficial microorganisms-plant-pathogen in the rhizosphere. However, the roles of organic acid components in this process have not been well studied. In this study the colonization of a plant growth-promoting rhizobacterium, Bacillus amyloliquefaciens SQR9, on cucumber root infected by Fusarium oxysporum f. sp. cucumerinum J. H. Owen (FOC) was investigated. Chemotaxis and biofilm formation response of SQR9 to root exudates and their organic acid components were analysed. Infection of FOC on cucumber had a positive effect (3.30-fold increase) on the root colonization of SQR9 compared with controls. Root secretion of citric acid (2.3 ± 0.2 μM) and fumaric acid (5.7 ± 0.5 μM) was enhanced in FOC-infected cucumber plants. Bacillus amyloliquefaciens SQR9 exhibited enhanced chemotaxis to root exudates of FOC-infected cucumber seedlings. Further experiments demonstrated that citric acid acts as a chemoattractant and fumaric acid as a stimulator of biofilm formation in this process. These results suggest that root exudates mediate the interaction of cucumber root and rhizosphere strain B. amyloliquefaciens SQR9 and enhance its root colonization. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Phylogeny, plant species, and plant diversity influence carbon use phenotypes among Fusarium populations in the rhizosphere microbiome

USDA-ARS?s Scientific Manuscript database

Carbon use by microorganisms in the rhizosphere microbiome has been linked to plant pathogen suppression and increased mineralization of soil nutrients for plant uptake, however factors that influence carbon use traits are poorly understood for most microbial groups. This work characterized the rela...

Mass spectrometry imaging: Towards mapping the elemental and molecular composition of the rhizosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veličković, Dušan; Anderton, Christopher R.

This short review will discuss and provide perspective into the utilization of mass spectrometry imaging (MSI) in studying the rhizosphere. It also serves to compliment the multi-omic focused review by White et al. in this journal issue, as MSI is capable of elucidating chemical distributions within samples of interest in an in situ fashions, and thus can provide spatial context to MS omics data in complementary experimental endeavors. The majority of reported MSI-based studies of plant-microbe interactions have focused on the phyllosphere and ‘associated rhizosphere’ (e.g., material that is not removed during harvesting), as sample preparation for these in situmore » analyses tends to be a limiting factor. These studies have provided valuable insight into the spatial arrangement of proteins, peptides, lipids, and other metabolites within these systems. We intend for this short review to be a primer about the history of MSI and its role in plant-microbe analysis. Along the way we reference many comprehensive reviews for the interested reader. Lastly, we offer a perspective on the future of MSI and its use in understanding the molecular transformations beyond what we coined as the ‘associated rhizosphere’ to the rest of rhizosphere zone and into the bulk soil.« less

Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions.

PubMed

Cipriano, Matheus A P; Lupatini, Manoeli; Lopes-Santos, Lucilene; da Silva, Márcio J; Roesch, Luiz F W; Destéfano, Suzete A L; Freitas, Sueli S; Kuramae, Eiko E

2016-12-01

Plant growth promoting rhizobacteria are well described and recommended for several crops worldwide. However, one of the most common problems in research into them is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition resulting from bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits, including phosphate solubilization, hormone production and antagonism to pathogen compounds, and their effect on plant growth under farm field conditions. Additionally, the impact of beneficial strains on the rhizospheric bacterial community was evaluated for inoculated plants. The strains IAC-RBcr4 and IAC-RBru1, with different plant growth promoting traits, improved lettuce plant biomass yields up to 30%. These two strains also impacted rhizosphere bacterial groups including Isosphaera and Pirellula (phylum Planctomycetes) and Acidothermus, Pseudolabrys and Singusphaera (phylum Actinobacteria). This is the first study to demonstrate consistent results for the effects of Pseudomonas strains on lettuce growth promotion for seedlings and plants grown under tropical field conditions. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

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

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. Copyright © 2015 Elsevier GmbH. All rights reserved.

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

Multiple antibiotic resistance patterns of rhizospheric bacteria isolated from Phragmites australis growing in constructed wetland for distillery effluent treatment.

PubMed

Chaturvedi, Sonal; Chandra, Ram; Rai, Vibhuti

2008-01-01

Susceptibility patterns of 12 different antibiotics were investigated against rhizospheric bacteria isolated from Phragmites australis from three different zones i.e. upper (0-5 cm), middle (5-10 cm), lower (10-15 cm) in constructed wetland system with and without distillery effluent. The major pollutants of distillery effluent were phenols, sulphide, heavy metals, and higher levels of biological oxygen demand (BOD), chemical oxygen demand (COD) etc. The antibiotic resistance properties of bacteria were correlated with the heavy metal tolerance (one of distillery pollutant). Twenty-two species from contaminated and seventeen species from non-contaminated site were tested by agar disc-diffusion method. The results revealed that more than 63% of total isolates were resistance towards one or more antibiotics tested from all the three different zones of contaminated sites. The multiple-drug resistance property was shown by total 8 isolates from effluent contaminated region out of which 3 isolates were from upper zone, 3 isolates from middle zone and 2 isolates were from lower zone. Results indicated that isolates from contaminated rhizosphere were found more resistant to antibiotics than isolates from non-contaminated rhizosphere. Further this study produces evidence suggesting that tolerance to antibiotics was acquired by isolates for the adaptation and detoxification of all the pollutants present in the effluent at contaminated site. This consequently facilitated the phytoremediation of effluent, which emerges the tolerance and increases resistance to antibiotics.

Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities.

PubMed

Pham, Hoang Nam; Michalet, Serge; Bodillis, Josselin; Nguyen, Tien Dat; Nguyen, Thi Kieu Oanh; Le, Thi Phuong Quynh; Haddad, Mohamed; Nazaret, Sylvie; Dijoux-Franca, Marie-Geneviève

2017-07-01

Plants adapt to metal stress by modifying their metabolism including the production of secondary metabolites in plant tissues. Such changes may impact the diversity and functions of plant associated microbial communities. Our study aimed to evaluate the influence of metals on the secondary metabolism of plants and the indirect impact on rhizosphere bacterial communities. We then compared the secondary metabolites of the hyperaccumulator Pteris vittata L. collected from a contaminated mining site to a non-contaminated site in Vietnam and identified the discriminant metabolites. Our data showed a significant increase in chlorogenic acid derivatives and A-type procyanidin in plant roots at the contaminated site. We hypothesized that the intensive production of these compounds could be part of the antioxidant defense mechanism in response to metals. In parallel, the structure and diversity of bulk soil and rhizosphere communities was studied using high-throughput sequencing. The results showed strong differences in bacterial composition, characterized by the dominance of Proteobacteria and Nitrospira in the contaminated bulk soil, and the enrichment of some potential human pathogens, i.e., Acinetobacter, Mycobacterium, and Cupriavidus in P. vittata's rhizosphere at the mining site. Overall, metal pollution modified the production of P. vittata secondary metabolites and altered the diversity and structure of bacterial communities. Further investigations are needed to understand whether the plant recruits specific bacteria to adapt to metal stress.

The diversity and abundance of phytase genes (β-propeller phytases) in bacterial communities of the maize rhizosphere.

PubMed

Cotta, S R; Cavalcante Franco Dias, A; Seldin, L; Andreote, F D; van Elsas, J D

2016-03-01

The ecology of microbial communities associated with organic phosphorus (P) mineralization in soils is still understudied. Here, we assessed the abundance and diversity of bacteria harbouring genes encoding β-propeller phytases (BPP) in the rhizosphere of traditional and transgenic maize cultivated in two Brazilian soils. We found a soil-dependent effect towards a higher abundance of phytase genes in the rhizosphere, and an absence of any impact of plant genotype. Phylogenetic analyses indicated members of the genera Pseudomonas, Caulobacter, Idiomarina and Maricaulis, close to 'uncultured bacteria', to constitute the dominant bacteria hosting this gene. The results obtained validate a methodology to target bacteria that are involved in the organic P cycle, and depict the responsiveness of such bacteria to the rhizosphere, albeit in dependency of the soil in which maize is cultivated. The data also identified the major bacterial groups that are associated with the organic P mineralization function. Micro-organisms play a key role in nutrient balance in soil ecosystems that are essential to life on the planet. However, some processes such as organic phosphorus mineralization, an important source of phosphorus supply in soil, is poorly studied mainly due the absence of an efficient methodology to assess the phytase-producing micro-organisms. In this study, a method to assess beta-propeller phytase (BPP)-carrying bacteria in soil was validated. This method may contribute to the knowledge of how these micro-organisms behave in the environment and contribute for plant growth promotion. © 2015 The Society for Applied Microbiology.

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees.

PubMed

Beckers, Bram; Op De Beeck, Michiel; Weyens, Nele; Boerjan, Wout; Vangronsveld, Jaco

2017-02-23

The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches. We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats. We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus. Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.

Experimental evidence of two mechanisms coupling leaf-level C assimilation to rhizosphere CO2 release

Treesearch

Zachary Kayler; Claudia Keitel; Kirstin Jansen; Arthur Gessler

2017-01-01

The time span needed for carbon fixed by plants to induce belowground responses of root and rhizosphere microbial metabolic processing is of high importance for quantifying the coupling between plant canopy physiology and soil biogeochemistry, but recent observations of a rapid link cannot be explained by new assimilate transport by phloem mass flow alone. We performed...

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

PubMed

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

2013-10-01

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

Microbiological and Geochemical Evidence of Fe(III) Reduction in the Rhizosphere (Root-Zone) of Wetland Plants

NASA Astrophysics Data System (ADS)

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

2002-05-01

We have found that the Fe-oxide deposits (Fe-plaque) on wetland plant roots contain abundant microbes including Fe(II)-oxidizing bacteria (FeOB) (Appl. Environ. Microbiol. 1999, 65:2758-2761). In the current study, we investigated the potential for root Fe-plaque to serve as a substrate for Fe(III)-reducing bacteria (FeRB) and compared rates of Fe reduction between plaque and bulk soil. In a study at six wetland habitats located in the Mid-Atlantic region, abundances of FeRB in the rhizosphere of Typha spp. and the bulk soil were enumerated using the most probable number technique. In the rhizosphere, FeRB accounted for an average of 12% of the total cell number while in the soil they accounted for <1% of the total bacteria. We subsequently performed a sequential chemical extraction on both roots and soil to determine if FeRB abundances were driven by differences in the reducibility of Fe(III) in each environment. The roots contained a significantly higher percentage of amorphous Fe (77.4%; p<0.05 n=5 wetlands) than the bulk soil (33.8%); conversely, the soil also had significantly higher amounts of crystalline Fe (41.1%, p<0.05, n=5 wetlands) than the roots (8.1%). A significant correlation was observed between the percentage of amorphous Fe and the percentage of FeRB (r2=0.583; p<0.05). Since amorphous Fe is more readily reduced by microbes than crystalline Fe, these results suggested that the roots provide a good substrate for iron-reducing bacteria. To determine how differences in reducible Fe(III) might limit Fe reduction potential, we performed 12-day anaerobic incubations of roots and soil with Geobacter metallireducans, a common FeRB isolated from aquatic environments. Although Fe(III) reduction rates peaked at between 48 and 72 hours in both the roots and soils, the total amount of Fe(II) production in the root samples was significantly higher than that in the soil samples (350 μ moles g dry weight-1 vs. 153 μ moles g dry weight-1; p<0.05). All of these

The effect of monoculture peanut and cassava/peanut intercropping on physical and chemical properties in peanut rhizosphere soil under the biochar application and straw mulching

NASA Astrophysics Data System (ADS)

Chen, X.; Tian, Y.; Guo, X. F.; Chen, G. K.; He, H. Z.; Li, H. S.

2017-03-01

Cassava/peanut intercropping is a popular cultivation method in the south China, with the advantage of apparent yield increase. In order to analyze the effect of cassava/peanut intercropping on physical and chemical properties in peanut rhizosphere soil, the physical and chemical properties were investigated under the biochar application and straw mulching. The result showed that the Ph, organic materials content, available phosphorus content, available potassium content in peanut rhizosphere under the biochar application increased by 7.06%, 94.52%, 17.53%, 25.08% (monoculture peanut) and 8.47%, 89.94%, 17.93%, 22.87% (cassava/peanut intercropping) compared with Ck in the same planting patterns. In addition, the available nitrogen content, organic materials content, available phosphorus content, and available potassium content in peanut rhizosphere under the straw mulching increased by 89.80%, 60.92%, 5.95%, 9.98% (monoculture peanut) and 67.09%, 52.34%, 6.96%, 11.94% (cassava/peanut intercropping) compared with Ck in the same planting patterns. In the same treatment conditions, bulk density in peanut rhizosphere soil decreased and porosity and saturated permeability coefficient increased slightly. But there was no significant difference between the two. At the same time, cassava/peanut intercropping could increase soil nutrients. Therefore, it is beneficial to apply biochar and straw mulching, and the suitable intercropping row spacing is more beneficial to increase soil nutrient contents.

Redox processes in the rhizosphere of restored peatlands - The impact of vascular plant species on electrochemical properties of dissolved organic matter

NASA Astrophysics Data System (ADS)

Agethen, Svenja; Wolff, Franziska; Knorr, Klaus-Holger

2016-04-01

Restoration of cut over peatlands in Central Europe is challenging in a landscape overused for agriculture. Excess nutrient availability by excess fertilization triggers uncharacteristic vegetation that is one key driver for carbon cycling. Those nutrient rich systems are often dominated by graminoids, and were often found to emit substantial amounts of methane. Plants grown under nutrient rich conditions provide more labile carbon in rhizodeposition and litter that fuels methanogenesis. Such species often have aerenchyma that facilitates direct CH4 emissions to the atmosphere and therefore impair the climate cooling function of bogs. On the other hand, aerenchymatic tissue supplies oxygen to the rhizosphere, which may reduce methanogenesis or stimulate methane oxidation, as methanogenesis is a strictly anaerobic process. Which of the effects prevail is often unclear. Therefore, the aim of this study was to test the impact of different vegetation on rhizospheric redox conditions and methanogenesis, including aerenchymatic vascular plants that are dominant in restored cut over peatlands. As ombrotrophic peat is poor in inorganic electron acceptors (EAs) to suppress methanogenesis, we analyzed the electron acceptor (EACs) and electron donor capacities (EDCs) of dissolved organic matter (DOM) in the rhizosphere to understand the impact of vegetation on anaerobic organic matter degradation. We planted Juncus effusus, Eriophorum vaginatum, Eriophorum angustifolium, Sphagnum (mixture of S. magellanicum, S. papillosum, S. sec. acutifolia, 1/3 each) plus non-vegetated controls; six replicates per batch; in containers with untreated homogenized peat. The plants grow under constant conditions (20° C, 12h diurnal light cycles and 80% RH). Anoxic conditions were achieved by keeping the water table at +10 cm. For monitoring, the rhizosphere is equipped with suction and gas samplers. We measure dissolved CO2 and CH4 concentrations, inorganic EAs (NO3-, Fe(III), and SO42-) and

Effects of Transgenic Bt+CpTI cotton on the abundance and diversity of rhizosphere ammonia oxidizing bacteria and archaea.

PubMed

Dong, Lianhua; Meng, Ying; Wang, Jing; Sun, Guoqing

2016-09-01

Genetically modified crops (GMCs) hold great promise for improving agricultural output, but at the same time present challenges in terms of environmental safety assessment. Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and archaea (AOA), are very important functional microbial groups in nitrogen cycle. The abundance and diversity of AOA and AOB in the rhizosphere of genetically modified cotton (SGK321) and non-GM cotton (SY321) across growth stages were investigated using real time quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Results showed that cotton genotype had a significant effect on the change in abundance of AOA and AOB, as indicated by amoA copy number. Variations in AOB abundance in rhizosphere of SY321 differed from those in SGK321. The number of AOB in the rhizosphere of SY321 fluctuated considerably: It dramatically decreased from 1.2?106 copies g-1 dry soil to 3?105 copies g-1 dry soil during the flowering stage and then increased to 1.1?106 copies g-1 and 1.5?106 copies g-1 at the belling and boll opening stages, respectively. However, abundance of AOB in the rhizosphere of SGK321 was relatively stable during all the stages of growth. The effect of SGK321 and SY321 on AOA number was quite similar to that of AOB: AOA abundance in SGK321 increased smoothly from 1.0 ?105 copies g-1 dry soil to 1.4?106 copies g-1 dry soil during growth, but that in SY321 fluctuated. Correspondence analysis (CA), canonical CA (CCA), and partial CCA (pCCA) of T-RFLP profiles of AOA and AOB showed that AOB community changed across growth stages in both cotton genotypes, and cotton genotype was the most important factor affecting the AOA community. In conclusion, the current findings indicated no adverse effect of GM cotton on functional microorganisms.

Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere.

PubMed

Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

2016-01-01

The use of Trichoderma isolates with efficient antagonistic activity represents a potentially effective and alternative disease management strategy to replace health hazardous chemical control. In this context, twenty isolates were obtained from tomato rhizosphere and evaluated by their antagonistic activity against four fungal pathogens ( Fusarium oxysporum f. sp. lycopersici , Alternaria alternata , Colletotrichum gloeosporoides and Rhizoctonia solani ). The production of extracellular cell wall degrading enzymes of tested isolates was also measured. All the isolates significantly reduced the mycelial growth of tested pathogens but the amount of growth reduction varied significantly as well. There was a positive correlation between the antagonistic capacity of Trichoderma isolates towards fungal pathogens and their lytic enzyme production. The Trichoderma isolates were initially sorted according to morphology and based on the translation elongation factor 1-α gene sequence similarity, the isolates were designated as Trichoderma harzianum , T. koningii , T. asperellum , T. virens and T. viride . PCA analysis explained 31.53, 61.95, 62.22 and 60.25% genetic variation among Trichoderma isolates based on RAPD, REP-, ERIC- and BOX element analysis, respectively. ERG - 1 gene, encoding a squalene epoxidase has been used for the first time for diversity analysis of antagonistic Trichoderma from tomato rhizosphere. Phylogenetic analysis of ERG -1 gene sequences revealed close relatedness of ERG -1sequences with earlier reported sequences of Hypocrea lixii , T. arundinaceum and T. reesei. However, ERG -1 gene also showed heterogeneity among some antagonistic isolates and indicated the possibility of occurrence of squalene epoxidase driven triterpene biosynthesis as an alternative biocontrol mechanism in Trichoderma species.

Characterization of rhizosphere bacteria for control of phytopathogenic fungi of tomato.

PubMed

Pastor, Nicolás; Carlier, Evelin; Andrés, Javier; Rosas, Susana B; Rovera, Marisa

2012-03-01

Fluorescent Pseudomonas spp., isolated from rhizosphere soil of tomato and pepper plants, were evaluated in vitro as potential antagonists of fungal pathogens. Strains were characterized using the API 20NE biochemical system, and tested against the causal agents of stem canker and leaf blight (Alternaria alternata f. sp. lycopersici), southern blight (Sclerotium rolfsii Sacc.), and root rot (Fusarium solani). To this end, dual culture antagonism assays were carried out on 25% Tryptic Soy Agar, King B medium, and Potato Dextrose Agar to determine the effect of the strains on mycelial growth of the pathogens. The effect of two concentrations of FeCl(3) on antagonism against Alternaria alternata f. sp. lycopersici was also tested. In addition, strains were screened for ability to produce exoenzymes and siderophores. Finally, the selected Pseudomonas strain, PCI2, was evaluated for effect on tomato seedling development and as a potential candidate for controlling tomato damping-off caused by Sclerotium rolfsii Sacc., under growth chamber conditions. All strains significantly inhibited Alternaria alternata f. sp. lycopersici, particularly in 25% TSA medium. Antagonistic effect on Sclerotium rolfsii Sacc. and Fusarium solani was greater on King B medium. Protease was produced by 30% of the strains, but no strains produced cellulase or chitinase. Growth chamber studies resulted in significant increases in plant stand as well as in root dry weight. PCI2 was able to establish and survive in tomato plants rhizosphere after 40 days following planting of bacterized seeds. Copyright © 2011 Elsevier Ltd. All rights reserved.

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L.).

PubMed

Umadevi, Palaniyandi; Anandaraj, Muthuswamy; Srivastav, Vivek; Benjamin, Sailas

2017-11-29

Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1.24e-12), Candidatus koribacter versatilis (p=2.66e-10)] and fungi [(Fusarium oxysporum (p=0.013), Talaromyces stipitatus (p=0.219) and Pestalotiopsis fici (p=0.443)] in terms of abundance in population and bacterial chemotaxis (p=0.012), iron metabolism (p=2.97e-5) with the reduction in abundance for pathogenicity islands (p=7.30e-3), phages and prophages (p=7.30e-3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p=2.34e-4), and degradation of heterocyclic aromatic compounds (p=3.59e-13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Bacterial physiological diversity in the rhizosphere of range plants in response to retorted shale stress. [Agropyron smithii Rydb; Atriplex canescens (Pursh) Nutt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metzger, W.C.; Klein, D.A.; Redente, E.F.

1986-10-01

Bacterial populations were isolated from the soil-root interface and root-free regions of Agropyron smithii Rydb. and Atriplex canescens (Pursh) Nutt. grown in soil, retorted shale, or soil over shale. Bacteria isolated from retorted shale exhibited a wider range of tolerance to alkalinity and salinity and decreased growth on amino acid substrates compared with bacteria from soil and soil-over-shale environments. Exoenzyme production was only slightly affected by growth medium treatment. Viable bacterial populations were higher in the rhizosphere and rhizoplane of plants grown in retorted shale than in plants grown in soil or soil over shale. In addition, a greater numbermore » of physiological groups of rhizosphere bacteria was observed in retorted shale, compared with soil alone. Two patterns of community similarity were observed in comparisons of bacteria from soil over shale with those from soil and retorted-shale environments. Root-associated populations from soil over shale had a higher proportion of physiological groups in common with those from the soil control than those from the retorted-shale treatment. However, in non-rhizosphere populations, bacterial groups from soil over shale more closely resembled the physiological groups from retorted shale.« less

Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.).

PubMed

Meng, Xianfa; Wang, Lin; Long, Xiaohua; Liu, Zhaopu; Zhang, Zhenhua; Zed, Rengel

2012-06-01

Diazotrophs in the soil may be influenced by plant factors as well as nitrogen (N) fertilization. In this study, we investigated potential diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) supplied with differing amounts of N. The community structure of N(2)-fixing bacteria was profiled using the length heterogeneity polymerase chain reaction (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP) based on a variation in the nifH gene. Higher numbers of diazotrophs were detected by T-RFLP compared to LH-PCR. The lowest number of N(2)-fixing bacteria was observed in the rhizosphere soil with high N fertilization. T-RFLP was a better method than LH-PCR for profiling microbial diversity of diazotrophs using multidimensional scaling (MDS) and analysis of similarity (ANOSIM) of fingerprints as well as diversity measures. The supply of N fertilizer appeared to negatively influence the abundance of diazotrophs in the rhizophere of the Jerusalem artichoke. Copyright © 2012 Institut Pasteur. All rights reserved.

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

Effect of reclaimed water effluent on bacterial community structure in the Typha angustifolia L. rhizosphere soil of urbanized riverside wetland, China.

PubMed

Huang, Xingru; Xiong, Wei; Liu, Wei; Guo, Xiaoyu

2017-05-01

In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal restriction fragment length polymorphism and 16S rRNA gene clone library. The results revealed significant spatial variation of bacterial communities along the river from upstream and downstream. For example, a higher relative abundance of γ-Proteobacteria, Firmicutes, Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria was detected at the downstream site compared to the upstream site. Additionally, with an increase of the reclaimed water interference intensity, the rhizosphere bacterial community showed a decrease in taxon richness, evenness and diversity. The relative abundance of bacteria closely related to the resistant of heavy-metal was markedly increased, while the bacteria related for carbon/nitrogen/phosphorus/sulfur cycling wasn't strikingly changed. Besides that, the pathogenic bacteria markedly increased in the downstream rhizosphere soil since reclaimed water supplement, while the possible plant growth-promoting rhizobacteria obviously reduced in the downstream sediment. Together these data suggest cause and effect between reclaimed water input into the wetland, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of contaminants. Copyright © 2016. Published by Elsevier B.V.

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.

Variation in phenolic root exudates and rhizosphere carbon cycling among tree species in temperate forest ecosystems

NASA Astrophysics Data System (ADS)

Zwetsloot, Marie; Bauerle, Taryn; Kessler, André; Wickings, Kyle

2017-04-01

Temperate forest tree species composition has been highly dynamic over the past few centuries and is expected to only further change under current climate change predictions. While aboveground changes in forest biodiversity have been widely studied, the impacts on belowground processes are far more challenging to measure. In particular, root exudation - the process through which roots release organic and inorganic compounds into the rhizosphere - has received little scientific attention yet may be the key to understanding root-facilitated carbon cycling in temperate forest ecosystems. The aim of this study was to analyze the extent by which tree species' variation in phenolic root exudate profiles influences soil carbon cycling in temperate forest ecosystems. In order to answer this question, we grew six temperate forest tree species in a greenhouse including Acer saccharum, Alnus rugosa, Fagus grandifolia, Picea abies, Pinus strobus, and Quercus rubra. To collect root exudates, trees were transferred to hydroponic growing systems for one week and then exposed to cellulose acetate strips in individual 800 mL jars with a sterile solution for 24 hours. We analyzed the methanol-extracted root exudates for phenolic composition with high-performance liquid chromatography (HPLC) and determined species differences in phenolic abundance, diversity and compound classes. This information was used to design the subsequent soil incubation study in which we tested the effect of different phenolic compound classes on rhizosphere carbon cycling using potassium hydroxide (KOH) traps to capture soil CO2 emissions. Our findings show that tree species show high variation in phenolic root exudate patterns and that these differences can significantly influence soil CO2 fluxes. These results stress the importance of linking belowground plant traits to ecosystem functioning. Moreover, this study highlights the need for research on root and rhizosphere processes in order to improve

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.

Rhizosphere hydrophobicity: A positive trait in the competition for water.

PubMed

Zeppenfeld, Thorsten; Balkenhol, Niko; Kóvacs, Kristóf; Carminati, Andrea

2017-01-01

The ability to acquire water from the soil is a major driver in interspecific plant competition and it depends on several root functional traits. One of these traits is the excretion of gel-like compounds (mucilage) that modify physical soil properties. Mucilage secreted by roots becomes hydrophobic upon drying, impedes the rewetting of the soil close to the root, the so called rhizosphere, and reduces water availability to plants. The function of rhizosphere hydrophobicity is not easily understandable when looking at a single plant, but it may constitute a competitive advantage at the ecosystem level. We hypothesize that by making the top soil hydrophobic, deep-rooted plants avoid competititon with shallow-rooted plants. To test this hypothesis we used an individual-based model to simulate water uptake and growth of two virtual plant species, one deep-rooted plant capable of making the soil hydrophobic and a shallow-rooted plant. We ran scenarios with different precipitation regimes ranging from dry to wet (350, 700, and 1400 mm total annual precipitation) and from high to low precipitation frequencies (1, 7, and 14 days). Plant species abundance and biomass were chosen as indicators for competitiveness of plant species. At constant precipitation frequency mucilage hydrophobicity lead to a benefit in biomass and abundance of the tap-rooted population. Under wet conditions this effect diminished and tap-rooted plants were less productive. Without this trait both species coexisted. The effect of root exudation trait remained constant under different precipitation frequencies. This study shows that mucilage secretion is a competitive trait for the acquisition of water. This advantage is achieved by the modification of the soil hydraulic properties and specifically by inducing water repellency in soil regions which are shared with other species.

Rhizosphere hydrophobicity: A positive trait in the competition for water

PubMed Central

Balkenhol, Niko; Kóvacs, Kristóf; Carminati, Andrea

2017-01-01

The ability to acquire water from the soil is a major driver in interspecific plant competition and it depends on several root functional traits. One of these traits is the excretion of gel-like compounds (mucilage) that modify physical soil properties. Mucilage secreted by roots becomes hydrophobic upon drying, impedes the rewetting of the soil close to the root, the so called rhizosphere, and reduces water availability to plants. The function of rhizosphere hydrophobicity is not easily understandable when looking at a single plant, but it may constitute a competitive advantage at the ecosystem level. We hypothesize that by making the top soil hydrophobic, deep-rooted plants avoid competititon with shallow-rooted plants. To test this hypothesis we used an individual-based model to simulate water uptake and growth of two virtual plant species, one deep-rooted plant capable of making the soil hydrophobic and a shallow-rooted plant. We ran scenarios with different precipitation regimes ranging from dry to wet (350, 700, and 1400 mm total annual precipitation) and from high to low precipitation frequencies (1, 7, and 14 days). Plant species abundance and biomass were chosen as indicators for competitiveness of plant species. At constant precipitation frequency mucilage hydrophobicity lead to a benefit in biomass and abundance of the tap-rooted population. Under wet conditions this effect diminished and tap-rooted plants were less productive. Without this trait both species coexisted. The effect of root exudation trait remained constant under different precipitation frequencies. This study shows that mucilage secretion is a competitive trait for the acquisition of water. This advantage is achieved by the modification of the soil hydraulic properties and specifically by inducing water repellency in soil regions which are shared with other species. PMID:28753673

Dynamics of ammonia-oxidizing communities in barley-planted bulk soil and rhizosphere following nitrate and ammonium fertilizer amendment.

PubMed

Glaser, Katrin; Hackl, Evelyn; Inselsbacher, Erich; Strauss, Joseph; Wanek, Wolfgang; Zechmeister-Boltenstern, Sophie; Sessitsch, Angela

2010-12-01

Oxidation of ammonia by nitrifying microorganisms is a major pathway that fertilizer nitrogen (N) may take upon application to agricultural soils, but the relative roles of bacterial (AOB) vs. archaeal (AOA) ammonia oxidizers are controversial. We explored the effects of various forms of mineral N fertilizer on the AOB and AOA community dynamics in two different soils planted with barley. Ammonia oxidizers were monitored via real-time PCR and terminal restriction fragment length polymorphism analysis of bacterial and archaeal amoA genes following the addition of either [NH₄]₂SO₄, NH₄NO₃ or KNO₃. AOB and AOA communities were also studied specifically in the rhizospheres of two different barley varieties upon [NH₄]₂SO₄ vs. KNO₃ addition. AOB changed in community composition and increased in abundance upon ammonium amendment in bulk soil and rhizosphere, with changes in bacterial amoA copy numbers lagging behind relative to changes in soil ammonium. In both soils, only T-RFs corresponding to phylotypes related to Nitrosospira clade 3a underwent significant community changes. Increases in AOB abundance were generally stronger in the bulk soil than in the rhizosphere, implying significant ammonia uptake by plant roots. AOA underwent shifts in the community composition over time and fluctuated in abundance in all treatments irrespective of ammonia availability. AOB were thus considered as the main agents responsible for fertilizer ammonium oxidation, while the functions of AOA in soil N cycling remain unresolved. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Key physiological properties contributing to rhizosphere adaptation and plant growth promotion abilities of Azospirillum brasilense.

PubMed

Fibach-Paldi, Sharon; Burdman, Saul; Okon, Yaacov

2012-01-01

Azospirillum brasilense is a plant growth promoting rhizobacterium (PGPR) that is being increasingly used in agriculture in a commercial scale. Recent research has elucidated key properties of A. brasilense that contribute to its ability to adapt to the rhizosphere habitat and to promote plant growth. They include synthesis of the auxin indole-3-acetic acid, nitric oxide, carotenoids, and a range of cell surface components as well as the ability to undergo phenotypic variation. Storage and utilization of polybetahydroxyalkanoate polymers are important for the shelf life of the bacteria in production of inoculants, products containing bacterial cells in a suitable carrier for agricultural use. Azospirillum brasilense is able to fix nitrogen, but despite some controversy, as judging from most systems evaluated so far, contribution of fixed nitrogen by this bacterium does not seem to play a major role in plant growth promotion. In this review, we focus on recent advances in the understanding of physiological properties of A. brasilense that are important for rhizosphere performance and successful interactions with plant roots. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Visualizing the impact of living roots on rhizosphere soil structure using X-ray microtomography

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2009-04-01

The rhizosphere is an interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 μm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

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

PubMed

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.

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

Biodegradation of propargite by Pseudomonas putida, isolated from tea rhizosphere.

PubMed

Sarkar, Soumik; Seenivasan, Subbiah; Asir, Robert Premkumar Samuel

2010-02-15

Biodegradation of miticide propargite was carried out in vitro by selected Pseudomonas strains isolated from tea rhizosphere. A total number of 13 strains were isolated and further screened based on their tolerance level to different concentrations of propargite. Five best strains were selected and further tested for their nutritional requirements. Among the different carbon sources tested glucose exhibited the highest growth promoting capacity and among nitrogen sources ammonium nitrate supported the growth to the maximum. The five selected Pseudomonas strain exhibited a range of degradation capabilities. Mineral salts medium (MSM) amended with glucose provided better environment for degradation with the highest degradation potential in strain SPR 13 followed by SPR 8 (71.9% and 69.0% respectively).

Root phenotypic differences across a historical gradient of wheat genotypes alter soil rhizosphere communities and their impact on nitrogen cycling

NASA Astrophysics Data System (ADS)

Kallenbach, C.; Junaidi, D.; Fonte, S.; Byrne, P. F.; Wallenstein, M. D.

2017-12-01

Plants and soil microorganisms can exhibit coevolutionary relationships where, for example, in exchange for root carbon, rhizosphere microbes enhance plant fitness through improved plant nutrient availability. Organic agriculture relies heavily on these interactions to enhance crop nitrogen (N) availability. However, modern agriculture and breeding under high mineral N fertilization may have disrupted these interactions through alterations to belowground carbon inputs and associated impacts on the soil microbiome. As sustainability initiatives lead to a restoration of agricultural soil organic matter, modern crop cultivars may still be constrained by crop roots' ability to effectively support microbial-mediated N mineralization. We investigated how differences in root traits across a historical gradient of spring wheat genotypes influence the rhizosphere microbial community and effects on soil N and wheat yield. Five genotypes, representing wild (Wild), pre-Green Revolution (Old), and modern (Modern) wheat, were grown under greenhouse conditions in soils with and without compost to also compare genotype response to difference in native soil microbiomes and organic resource availability. We analyzed rhizosphere soils for microbial community composition, enzyme activities, inorganic N, and microbial biomass. Root length density, surface area, fine root volume and root:shoot ratio were higher in the Wild and Old genotype (Gypsum) compared to the two Modern genotypes (P<0.01). The Wild and Old genotype had a more positive response to compost for root length and diameter, N-cycling enzyme activities, microbial biomass, and soil inorganic N, compared to Modern genotypes. However, under unamended soils, the microbial community and soil N were not affected by genotypes. We also relate how root traits and N cycling across genotypes correspond to microbial community composition. Our preliminary data suggest that the older wheat genotypes and their root traits are more

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

PubMed

Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

2015-01-01

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

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

Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.).

PubMed

Babić, Katarina Huić; Schauss, Kristina; Hai, Brigitte; Sikora, Sanja; Redzepović, Sulejman; Radl, Viviane; Schloter, Michael

2008-11-01

Inoculation of leguminous seeds with selected rhizobial strains is practised in agriculture to ameliorate the plant yield by enhanced root nodulation and nitrogen uptake of the plant. However, effective symbiosis between legumes and rhizobia does not only depend on the capacity of nitrogen fixation but also on the entire nitrogen turnover in the rhizosphere. We investigated the influence of seed inoculation with two indigenous Sinorhizobium meliloti strains exhibiting different efficiency concerning plant growth promotion on nitrogen turnover processes in the rhizosphere during the growth of alfalfa. Quantification of six target genes (bacterial amoA, nirK, nirS, nosZ, nifH and archaeal amoA) within the nitrogen cycle was performed in rhizosphere samples before nodule formation, at bud development and at the late flowering stage. The results clearly demonstrated that effectiveness of rhizobial inocula is related to abundance of nifH genes in the late flowering phase of alfalfa. Moreover, other genes involved in nitrogen turnover had been affected by the inocula, e.g. higher numbers of amoA copies were observed during flowering when the more effective strain had been inoculated. However, the respective gene abundances differed overall to a greater extent between the three plant development stages than between the inoculation variants.

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.

Imaging pH and oxygen at the soil-root interface by planar optodes: a challenging technology to study dynamic rhizosphere processes.

NASA Astrophysics Data System (ADS)

Daudin, Gabrielle; Oburger, Eva; Schmidt, Hannes; Borisov, Sergey; Pradier, Céline; Jourdan, Christophe; Marsden, Claire; Obermaier, Daniela; Woebken, Dagmar; Richter, Andreas; Wenzel, Walter; Hinsinger, Philippe

2017-04-01

Roots do not only take up water and nutrients from surrounding soil but they also release a wide range of exudates, such as low molecular weight organic compounds, CO2 or protons. Root-soil interactions trigger heterogeneous rhizosphere processes based on differences in root activity along the root axis and with distance from the root surface. Elucidating their temporal and spatial dynamics is of crucial importance for a better understanding of these interrelated biogeochemical processes in the rhizosphere. Therefore, monitoring key parameters at a fine scale and in a non-invasive way at the root-soil interface is essential. Planar optodes are an emerging technology that allows in situ and non-destructive imaging of mainly pH, CO2 and O2. Originated in limnology, planar optodes have recently been applied to soil-root systems in laboratory conditions. This presentation will highlight advantages and challenges of using planar optodes to image pH and O2 dynamics in the rhizosphere, focusing on two RGB (red-green-blue) approaches: a commercially available system (PreSens) and a custom-made one. Important insights into robustness, accuracy, potentials and limitations of the two systems applied to different laboratory/greenhouse-based experimental conditions (flooded and aerobic rhizobox systems, plant species) will be addressed. Furthermore, challenges of optode measurements in the field, including a first case study with Eucalyptus grandis in Brazil, will be discussed.

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities--A Comparison between Chemical Fertilizers and Bioinoculants.

PubMed

Gupta, Rashi; Bisaria, V S; Sharma, Shilpi

2015-01-01

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, with that of application of chemical fertilizers on plant's growth parameters and its rhizospheric microbial communities. Real-time PCR assay was carried out to target the structure (16S rRNA) and function (nitrogen cycle) of rhizospheric microbiota, using both DNA and RNA as markers. The results showed that the microbial consortium was the most efficient in increasing grain yield (2.5-fold), even better than the recommended dose of chemical fertilizers (by 1.2-fold) and showed enhancement in nifH and amoA transcripts by 2.7- and 2.0-fold, respectively. No adverse effects of bioinoculants' application were observed over the rhizospheric microbial community, rendering the consortium to be safe for release in agricultural fields.

Copper-tolerant rhizosphere bacteria-characterization and assessment of plant growth promoting factors.

PubMed

Rathi, Manohari; Nandabalan, Yogalakshmi Kadapakkam

2017-04-01

Remediation of heavy metal contaminated soil is a major problem or concern worldwide. Heavy metal accumulation in the soil is increasing day by day by industries, mines, agriculture, fuel combustion and municipal waste discharge. Such contaminated soils harbour a large number of resistant microbial populations. Screening and isolation of such microbes would be utilized for natural remediation of metal contaminated soils. Therefore, in the present study, highly copper-tolerant bacteria from rhizosphere soil of Cynodon dactylon grown in brass effluent contaminated soil were isolated and assessed for plant growth promoting factors. A total of 61 isolates were isolated from the rhizosphere of three contaminated sites. Six highly copper-tolerant isolates named as MYS1, MYS2, MYS3, MYS4, MYS5 and MYS6 were isolated through enrichment in copper containing nutrient broth. 16S rRNA analysis revealed that the isolates were from genera Stenotrophomonas and Brevundimonas and belong to classes Alpha Proteobacteriacea and Gamma Proteobacteriacea, respectively. Strain MYS1, MYS2 and MYS4 showed 95-99% similarity with Stenotrophomonas acidaminiphila, strain MYS3 and MYS5 showed 99 and 97% similarity with Stenotrophomonas maltophilia and Stenotrophomonas sp. Strain MYS6 showed 94% similarity with Brevundimonas diminuta. All the rhizobacteria showed plant growth promoting traits such as production of siderophores, indole acetic acid (IAA), phosphate solubilization and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. From this study, we can conclude that all the isolates possess copper resistance and potential for phytoremediation of copper polluted soils.

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea--A Metagenomic Approach.

PubMed

Simões, Marta Filipa; Antunes, André; Ottoni, Cristiane A; Amini, Mohammad Shoaib; Alam, Intikhab; Alzubaidy, Hanin; Mokhtar, Noor-Azlin; Archer, John A C; Bajic, Vladimir B

2015-10-01

Covering a quarter of the world's tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%-85%), while Basidiomycota was less abundant (14%-24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Contrasting Effects of Cattle Manure Applications and Root-Induced Changes on Heavy Metal Dynamics in the Rhizosphere of Soybean in an Acidic Haplic Fluvisol: A Chronological Pot Experiment.

PubMed

Chu, Qingnan; Sha, Zhimin; Osaki, Mitsuru; Watanabe, Toshihiro

2017-04-19

To characterize the dynamic mobilization of heavy metals (HM) in a crop-soil system affected by cattle manure (CM) application, soybean [Glycine max L. Merr. cv. Toyoharuka] crops were exposed in a chronological pot experiment to three CM application rates and sampled at two vegetative stages and two reproductive stages. A sequential extraction procedure for metal fractionation, soil pH, microbial activity, and plant HM uptake was determined. In non-rhizopshere soil, with CM application a liming effect was detected, and increased microbial activity was detected at the reproductive stage. CM application shifted Cd from available state to oxide-bound pool in non-rhizosphere soil; however, shifts in Cd from an oxide-bound pool to the available state were observed in rhizosphere soil. CM application stabilized the available Zn and Pb to oxide-bound Zn and organic-bound Pb in both non-rhizosphere and rhizosphere soils, and the stabilizing degree increased with higher CM application rates. The promoted Zn immobilization in the rhizosphere was due to the liming effects induced by added CM that counteracted the root-induced acidification. On the basis of a stepwise multiple regression analysis, the shift of Cd and Pb fractionation was mainly related to microbial activity. Adding manure inhibited Zn and Pb uptake but promoted Cd uptake by soybean, and a greater influence was detected at the reproductive stage, at which CM application increased the root Cd-absorbing power but did not significantly affect the Zn- and Pb-absorbing powers. In an agricultural context, long-term CM application, even at the recommended rate of 10.13 Mg ha -1 , may cause a soybean Zn deficiency and high Pb accumulation in Haplic Fluvisols, although CM is often considered as an environmentally friendly fertilizer.

Fungal diversity, dominance, and community structure in the rhizosphere of clonal Picea mariana plants throughout nursery production chronosequences.

PubMed

Vujanovic, V; Hamelin, R C; Bernier, L; Vujanovic, G; St-Arnaud, M

2007-11-01

Fungal diversity in the rhizosphere of healthy and diseased clonal black spruce (Picea mariana) plants was analyzed with regard to nursery production chronosequences. The four key production stages were sampled: mother plants (MP), 8-week-old cuttings (B + 0), second-year cuttings (B + 1), and third-year cuttings (B + 2). A total of 45 fungal taxa were isolated and identified based on cultural, phenotypic, and molecular characters. Members of phylum Ascomycota dominated, followed by Basidiomycota and Zygomycota. Diagnosis characters and distance analysis of the internal transcribed spacer rDNA sequences allowed the identification of 39 ascomycetous taxa. Many belong to the order Hypocreales, families Hypocreaceae and Nectriaceae, which contain many clusters of potentially pathogenic taxa (Cylindrocladium, Fusarium, and Neonectria) and are also ecologically associated with antagonistic taxa (Chaetomium, Hypocrea, Microsphaeropsis, Penicillium, Paecilomyces, Verticillium, Trichoderma, and Sporothrix). This is also the first report of a Cylindrocladium canadense association with disease symptoms and relation with Pestalotiopsis, Fusarium, Exserochilum, Rhizoctonia, and Xenochalara fungal consortia. Both production chronosequence and plant health considerably influenced fungal taxa assemblages. Unweighted pair-group arithmetic average clustering showed that isolates from MP, B + 0, and B + 1 plant rhizospheres clustered together within healthy or diseased health classes, whereas isolates from healthy and diseased B + 2 plants clustered together. Canonical correspondence analysis revealed substantial alteration in community assemblages with regard to plant health and yielded a principal axis direction that regrouped taxa associated with diseased plant rhizosphere soil, whereas the opposite axis direction was associated with healthy plants. Two diversity indices were defined and applied to assess the fungal taxa contribution (Tc) and persistence (Pi) throughout the

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

PubMed

Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong

2017-06-01

The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.

Elevated CO2 increases glomalin-related soil protein (GRSP) in the rhizosphere of Robinia pseudoacacia L. seedlings in Pb- and Cd-contaminated soils.

PubMed

Jia, Xia; Zhao, Yonghua; Liu, Tuo; Huang, Shuping; Chang, Yafei

2016-11-01

Glomalin-related soil protein (GRSP), which contains glycoproteins produced by arbuscular mycorrhizal fungi (AMF), as well as non-mycorrhizal-related heat-stable proteins, lipids, and humic materials, is generally categorized into two fractions: easily extractable GRSP (EE-GRSP) and total GRSP (T-GRSP). GRSP plays an important role in soil carbon (C) sequestration and can stabilize heavy metals such as lead (Pb), cadmium (Cd), and manganese (Mn). Soil contamination by heavy metals is occurring in conjunction with rising atmospheric CO 2 in natural ecosystems due to human activities. However, the response of GRSP to elevated CO 2 combined with heavy metal contamination has not been widely reported. Here, we investigated the response of GRSP to elevated CO 2 in the rhizosphere of Robinia pseudoacacia L. seedlings in Pb- and Cd-contaminated soils. Elevated CO 2 (700 μmol mol -1 ) significantly increased T- and EE- GRSP concentrations in soils contaminated with Cd, Pb or Cd + Pb. GRSP contributed more carbon to the rhizosphere soil organic carbon pool under elevated CO 2  + heavy metals than under ambient CO 2 . The amount of Cd and Pb bound to GRSP was significantly higher under elevated (compared to ambient) CO 2 ; and elevated CO 2 increased the ratio of GRSP-bound Cd and Pb to total Cd and Pb. However, available Cd and Pb in rhizosphere soil under increased elevated CO 2 compared to ambient CO 2 . The combination of both metals and elevated CO 2 led to a significant increase in available Pb in rhizosphere soil compared to the Pb treatment alone. In conclusion, increased GRSP produced under elevated CO 2 could contribute to sequestration of soil pollutants by adsorption of Cd and Pb. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact of pyrometallurgical slags on sunflower growth, metal accumulation and rhizosphere microbial communities.

PubMed

Agnello, A C; Potysz, A; Fourdrin, C; Huguenot, D; Chauhan, P S

2018-06-05

Metallurgical exploitation originates metal-rich by-products termed slags, which are often disposed in the environment being a source of heavy metal pollution. Despite the environmental risk that this may pose for living organisms, little is known about the impact of slags on biotic components of the ecosystem like plants and rhizosphere microbial communities. In this study, metal-rich (Cu, Pb, Zn) granulated slags (GS) derived from Cu production process, were used for a leaching test in the presence of the soil pore solution, showing that soil solution enhanced the release of Cu from GS. A pot experiment was conducted using as growing substrate for sunflower (Helianthus annuus) a 50% w/w mix of an agricultural soil and GS. Bioavailability of metals in soil was, in increasing order: Pb < Zn < Cu. Sunflower was able to grow in the presence of GS and accumulated metals preferentially in above-ground tissues. Microbial diversity was assessed in rhizosphere and bulk soil using community level physiological profiling (CLPP) and 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) analyses, which demonstrated a shift in the diversity of microbial communities induced by GS. Overall, these results suggest that metallurgical wastes should not be considered inert when dumped in the soil. Implications from this study are expected to contribute to the development of sustainable practices for the management of pyrometallurgical slags, possibly involving a phytomanagement approach. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

[Effects of intercropping Chinese milk vetch on functional characteristics of soil microbial community in rape rhizosphere].

PubMed

Zhou, Quan; Wang, Long Chang; Xing, Yi; Ma, Shu Min; Zhang, Xiao Duan; Chen, Jiao; Shi, Chao

2018-03-01

The application of green manure is facing serious problems in purple soil region of southwest China. With the aim to explore the potential application of green manure, we examined the functional characteristics of soil microbial community in a system of Chinese milk vetch intercropped with rape. The innovations are the application of Chinese milk vetch in dry land of the southwest China and the establishment of new planting pattern of rape by providing empirical data. Results showed that the intercropping with Chinese milk vetch decreased the carbon resource use efficiency of microbial community in rape rhizosphere, especially for the utilization of carbohydrates. At the same time, Shannon index, Simpson index, and richness were reduced, but evenness index was increased by intercropping. Those results from cluster analysis and principal component analysis suggest that the soil microbial community composition was significantly different between monocropping and intercropping. The carbohydrates, amino acids and carboxylic acids were the sensitive carbon sources for differentiating the changes of the microbial community induced by monocropping and intercropping. Intercropping Chinese milk vetch could decrease functional activity, change community composition, and reduce diversity of soil microbial community in rape rhizosphere.

Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium.

PubMed

Gkorezis, Panagiotis; Bottos, Eric M; Van Hamme, Jonathan D; Franzetti, Andrea; Abbamondi, Gennaro Roberto; Balseiro-Romero, Maria; Weyens, Nele; Rineau, Francois; Vangronsveld, Jaco

2015-08-13

The 3.94-Mb draft genome of Acinetobacter calcoaceticus GK1, a hydrocarbonoclastic plant growth-promoting Gram-negative rhizospheric bacterium, is presented here. Isolated at the Ford Motor Company site in Genk, Belgium, from poplar trees planted on a diesel-contaminated plume, GK1 is useful for enhancing hydrocarbon phytoremediation. Copyright © 2015 Gkorezis et al.

Determination of mannitol sorbitol and myo-inositol in olive tree roots and rhizospheric soil by gas chromatography and effect of severe drought conditions on their profiles.

PubMed

Mechri, Beligh; Tekaya, Meriem; Cheheb, Hechmi; Hammami, Mohamed

2015-01-01

This study reports a method for the analysis of mannitol, sorbitol and myo-inositol in olive tree roots and rhizospheric soil with gas chromatography. The analytical method consists of extraction with a mixture of dichloromethane:methanol (2:1, v/v) for soil samples and a mixture of ethanol:water (80:20) for root samples, silylation using pyridine, hexamethyldisilazane (HMDS) and trimethylchlorosilane (TMCS). The recovery of mannitol sorbitol and myo-inositol (for extraction and analysis in dichloromethane:methanol and ethanol:water) was acceptable and ranged from 100.3 to 114.7%. The time of analysis was <24 min. Among identified polyols extracted from rhizosphere and roots of olive plants, mannitol was the major compound. A marked increase in mannitol content occurred in rhizosphere and roots of water-stressed plants, suggesting a much broader role of mannitol in stress response based on its ability to act as a compatible solute. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Uranium Immobilization in an Iron-Rich Rhizosphere of a Native Wetland Plant from the Savannah River Site under Reducing Conditions

EPA Science Inventory

The hypothesis of this study was that iron plaque formed on the roots of wetland plants and their rhizospheres create environmental conditions favorable for iron reducing bacteria that promote the in situ immobilization of uranium. Greenhouse microcosm studies were conducted usin...

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

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

Effect of citric acid and rhizosphere bacteria on metal plaque formation and metal accumulation in reeds in synthetic acid mine drainage solution.

PubMed

Guo, Lin; Cutright, Teresa J

2014-06-01

Many of regions in the world have been affected by acid mine drainage (AMD). The study assessed the effect of rhizosphere bacteria and citric acid (CA) on the metal plaque formation and heavy metal uptake in Phragmites australis cultured in synthetic AMD solution. Mn and Al plaque were not formed, but Fe plaque which was mediated by rhizosphere iron oxidizing bacteria (Fe(II)OB) was observed on the root system of reeds. Fe plaque did not significantly influence the uptake of Fe, Al and Mn into tissues of reeds. CA significantly (p<0.01) inhibited the growth of Fe(II)OB and decreased the formation of Fe plaque. CA also significantly improved (p<0.05) the accumulation of Fe, Mn and Al in all the tissues of reeds. Roots and rhizomes were the main organs to store metals. The roots contained 0.08±0.01mg/g Mn, 2.39±0.26mg/g Fe and 0.19±0.02mg/g Al, while the shoots accumulated 0.04±0.00mg/g Mn, 0.20±0.01mg/g Fe, 0.11±0.00mg/g Al in reeds cultured in solution amended with 2.101g/l CA and without inoculation of rhizosphere bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants

PubMed Central

Gupta, Rashi; Bisaria, V. S.; Sharma, Shilpi

2015-01-01

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, with that of application of chemical fertilizers on plant’s growth parameters and its rhizospheric microbial communities. Real-time PCR assay was carried out to target the structure (16S rRNA) and function (nitrogen cycle) of rhizospheric microbiota, using both DNA and RNA as markers. The results showed that the microbial consortium was the most efficient in increasing grain yield (2.5-fold), even better than the recommended dose of chemical fertilizers (by 1.2-fold) and showed enhancement in nifH and amoA transcripts by 2.7- and 2.0-fold, respectively. No adverse effects of bioinoculants' application were observed over the rhizospheric microbial community, rendering the consortium to be safe for release in agricultural fields. PMID:26231030

Transfer of radiocesium from rhizosphere soil to four cruciferous vegetables in association with a Bacillus pumilus strain and root exudation.

PubMed

Aung, Han Phyo; Mensah, Akwasi Dwira; Aye, Yi Swe; Djedidi, Salem; Oikawa, Yosei; Yokoyama, Tadashi; Suzuki, Sohzoh; Dorothea Bellingrath-Kimura, Sonoko

2016-11-01

This study was carried out to assess the effect of Bacillus pumilus on the roots of four cruciferous vegetables with different root structures in regard to enhancement of 137 Cs bioavailability in contaminated rhizosphere soil. Results revealed that B. pumilus inoculation did not enhance the plant biomass of vegetables, although it increased root volume and root surface areas of all vegetables except turnip. The pH changes due to rhizosphere acidification by B. pumilus inoculation and root exudation did not affect the bioavailability of 137 Cs. However, concentrations of 137 Cs in plant tissues and soil-to-plant transfer values increased as a result of the larger root volume and root surface area of vegetables due to inoculation. Moreover, leafy vegetables, which possessed larger root volume and root surface areas, had a higher 137 Cs transfer value than root vegetables. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Proliferation of the biocontrol agent Fusarium oxysporum f. sp. strigae and its impact on indigenous rhizosphere fungal communities in maize under different agro-ecologies.

PubMed

Zimmermann, Judith; Musyoki, Mary K; Cadisch, Georg; Rasche, Frank

2016-06-01

Our objectives were to (1) monitor the proliferation of the biocontrol agent (BCA) Fusarium oxysporum f. sp. strigae strain "Foxy-2", an effective soil-borne BCA against the parasitic weed Striga hermonthica , in the rhizosphere of maize under different agro-ecologies, and (2) investigate its impact on indigenous rhizosphere fungal community abundance and composition. Field experiments were conducted in Busia and Homa Bay districts in western Kenya during two cropping seasons to account for effects of soil type, climate, growth stage and seasonality. Maize seeds were coated with or without "Foxy-2" and soils were artificially infested with S. hermonthica seeds. One treatment with nitrogen rich organic residues ( Tithonia diversifolia ) was established to compensate hypothesized resource competition between "Foxy-2" and the indigenous fungal community. Rhizosphere soil samples collected at three growth stages (i.e., EC30, EC60, EC90) of maize were subjected to abundance measurement of "Foxy-2" and total indigenous fungi using quantitative polymerase chain reaction (qPCR) analysis. Terminal restriction fragment length polymorphism (TRFLP) analysis was used to assess potential alterations in the fungal community composition in response to "Foxy-2" presence. "Foxy-2" proliferated stronger in the soils with a sandy clay texture (Busia) than in those with a loamy sand texture (Homa Bay) and revealed slightly higher abundance in the second season. "Foxy-2" had, however, only a transient suppressive effect on total indigenous fungal abundance which ceased in the second season and was further markedly compensated after addition of T. diversifolia residues. Likewise, community structure of the indigenous fungal community was mainly altered by maize growth stages, but not by "Foxy-2". In conclusion, no adverse effects of "Foxy-2" inoculation on indigenous fungal rhizosphere communities were observed corroborating the safety of this BCA under the given agro-ecologies.

Plant-Sediment Interactions in Salt Marshes - An Optode Imaging Study of O2, pH, and CO 2 Gradients in the Rhizosphere.

PubMed

Koop-Jakobsen, Ketil; Mueller, Peter; Meier, Robert J; Liebsch, Gregor; Jensen, Kai

2018-01-01

In many wetland plants, belowground transport of O 2 via aerenchyma tissue and subsequent O 2 loss across root surfaces generates small oxic root zones at depth in the rhizosphere with important consequences for carbon and nutrient cycling. This study demonstrates how roots of the intertidal salt-marsh plant Spartina anglica affect not only O 2 , but also pH and CO 2 dynamics, resulting in distinct gradients of O 2 , pH, and CO 2 in the rhizosphere. A novel planar optode system (VisiSens TD ® , PreSens GmbH) was used for taking high-resolution 2D-images of the O 2 , pH, and CO 2 distribution around roots during alternating light-dark cycles. Belowground sediment oxygenation was detected in the immediate vicinity of the roots, resulting in oxic root zones with a 1.7 mm radius from the root surface. CO 2 accumulated around the roots, reaching a concentration up to threefold higher than the background concentration, and generally affected a larger area within a radius of 12.6 mm from the root surface. This contributed to a lowering of pH by 0.6 units around the roots. The O 2 , pH, and CO 2 distribution was recorded on the same individual roots over diurnal light cycles in order to investigate the interlinkage between sediment oxygenation and CO 2 and pH patterns. In the rhizosphere, oxic root zones showed higher oxygen concentrations during illumination of the aboveground biomass. In darkness, intraspecific differences were observed, where some plants maintained oxic root zones in darkness, while others did not. However, the temporal variation in sediment oxygenation was not reflected in the temporal variations of pH and CO 2 around the roots, which were unaffected by changing light conditions at all times. This demonstrates that plant-mediated sediment oxygenation fueling microbial decomposition and chemical oxidation has limited impact on the dynamics of pH and CO 2 in S. anglica rhizospheres, which may in turn be controlled by other processes such as root

Mrt, a Gene Unique to Fungi, Encodes an Oligosaccharide Transporter and Facilitates Rhizosphere Competency in Metarhizium robertsii1[C][W

PubMed Central

Fang, Weiguo; St. Leger, Raymond J.

2010-01-01

The symbiotic associations between rhizospheric fungi and plants have enormous environmental impact. Fungi are crucial to plant health as antagonists of pathogens and herbivores and facilitate the uptake of soil nutrients. However, little is known about the plant products obtained by fungi in exchange or how they are transported through the symbiotic interface. Here, we demonstrate that sucrose and raffinose family oligosaccharides in root exudates are important for rhizosphere competence in the insect pathogen Metarhizium robertsii (formerly known as Metarhizium anisopliae). We identified mutants in the Metarhizium raffinose transporter (Mrt) gene of M. robertsii that grew poorly in root exudate and were greatly reduced in rhizosphere competence on grass roots. Studies on sugar uptake, including competition assays, revealed that MRT was a sucrose and galactoside transporter. Disrupting MRT resulted in greatly reduced or no growth on sucrose and galactosides but did not affect growth on monosaccharides or oligosaccharides composed entirely of glucose subunits. Consistent with this, expression of Mrt is exclusively up-regulated by galactosides and sucrose. Expressing a green fluorescent protein gene under the control of the Mrt promoter confirmed that MRT was expressed by germlings in the vicinity of grass roots but not in surrounding bulk soil. Disrupting Mrt did not reduce virulence to insects, demonstrating that Mrt is exclusively involved in M. robertsii’s interactions with plants. To our knowledge, MRT is the first oligosaccharide transporter identified and characterized in a fungus and is unique to filamentous fungi, but homologous genes in Magnaporthe, Ustilago, Aspergillus, Fusarium, Epichloe, and Penicillium species indicate that oligosaccharide transport is of widespread significance. PMID:20837701

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

PubMed

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

2016-07-15

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. 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 indicated stable

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.

Aluminium-phosphate interactions in the rhizosphere of two bean species: Phaseolus lunatus L. and Phaseolus vulgaris L.

PubMed

Mimmo, Tanja; Ghizzi, Massimiliano; Cesco, Stefano; Tomasi, Nicola; Pinton, Roberto; Puschenreiter, Markus

2013-12-01

Plants differ in their response to high aluminium (Al) concentrations, which typically cause toxicity in plants grown on acidic soils. The response depends on plant species and environmental conditions such as substrate and cultivation system. The present study aimed to assess Al-phosphate (P) dynamics in the rhizosphere of two bean species, Phaseolus vulgaris L. var. Red Kidney and Phaseolus lunatus L., in rhizobox experiments. Root activity of the bean species induced up to a sevenfold increase in exchangeable Al and up to a 30-fold decrease in extractable P. High soluble Al concentrations triggered the release of plant-specific carboxylates, which differed between soil type and plant species. The results suggest that P. vulgaris L. mitigates Al stress by an internal defence mechanism and P. lunatus L. by an external one, both mechanisms involving organic acids. Rhizosphere mechanisms involved in Al detoxification were found to be different for P. vulgaris L. and P. lunatus L., suggesting that these processes are plant species-specific. Phaseolus vulgaris L. accumulates Al in the shoots (internal tolerance mechanism), while P. lunatus L. prevents Al uptake by releasing organic acids (exclusion mechanism) into the growth media. © 2013 Society of Chemical Industry.

Pesticide dissipation and microbial community changes in a biopurification system: influence of the rhizosphere.

PubMed

Diez, M C; Elgueta, S; Rubilar, O; Tortella, G R; Schalchli, H; Bornhardt, C; Gallardo, F

2017-12-01

The dissipation of atrazine, chlorpyrifos and iprodione in a biopurification system and changes in the microbial and some biological parameters influenced by the rhizosphere of Lolium perenne were studied in a column system packed with an organic biomixture. Three column depths were analyzed for residual pesticides, peroxidase, fluorescein diacetate activity and microbial communities. Fungal colonization was analyzed by confocal laser scanning microscopy to assess the extent of its proliferation in wheat straw. The L. perenne rhizosphere enhanced pesticide dissipation and negligible pesticide residues were detected at 20-30 cm column depth. Atrazine, chlorpyrifos and iprodione removal was 82, 89 and 74% respectively in the first 10 cm depth for columns with vegetal cover. The presence of L. perenne in contaminated columns stimulated peroxidase activity in all three column depth sections. Fluorescein diacetate activity decreased over time in all column sections with the highest values in biomixtures with vegetal cover. Microbial communities, analyzed by PCR-DGGE, were not affected by the pesticide mixture application, presenting high values of similarity (>65%) with and without vegetal cover. Microbial abundance of Actinobacteria varied according to treatment and no clear link was observed. However, bacterial abundance increased over time and was similar with and without vegetal cover. On the other hand, fungal abundance decreased in all sections of columns after 40 days, but an increase was observed in response to pesticide application. Fungal colonization and straw degradation during pesticide dissipation were verified by monitoring the lignin autofluorescence loss.

[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. Copyright © 2016 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

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

[Effects of elevated ozone concentrations on enzyme activities and organic acids content in wheat rhizospheric soil.

PubMed

Yin, Wei Qin; Jing, Hao Qi; Wang, Ya Bo; Wei, Si Yu; Sun, Yue; Wang, Sheng Sen; Wang, Xuai Zhi

2018-02-01

The elevated concentration of tropospheric ozone (O 3 ) is an important global climate change driver, with adverse impacts on soil ecological environment and crop growth. In this study, a pot experiment was carried out in an open top chamber (OTC), to investigate the effects of elevated ozone concentration on soil enzyme activities (catalase, polyphenol oxidase, dehydrogenase and invertase), organic acids contents (oxalic acid, citric acid and malic acid) at different growth stages (tillering, jointing, heading and ripening stages) of wheat, and combined with the rhizospheric soil physicochemical properties and plant root characteristics to analyze the underlying reasons. The results showed that, elevated ozone concentration increased soil catalase, polyphenol oxidase, dehydrogenase and invertase activities at wheat ripening period to different degrees, with the effects on the activities of catalase and polyphenol oxidase being statistically significant. At the heading stage, activities of dehydrogenase and invertase were significantly increased by up to 76.7%. At the ripening stage, elevated ozone concentration significantly increased the content of citric acid and malic acid and redox potential (Eh) in rhizospheric soil, but reduced soil pH, electrical conductivity, total carbon and nitrogen. For root characteristics, elevated ozone concentrations significantly reduced the wheat root biomass, total root length and root surface area but increased the average root diameter.

Peudomonas fluorescens diversity and abundance in the rhizosphere

NASA Astrophysics Data System (ADS)

Amina, Melinai; Ahmed, Bensoltane; Khaladi, Mederbel

2010-05-01