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

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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

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

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Peng Liu

2015-01-01

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

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

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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.

Pseudomonas community structure and antagonistic potential in the rhizosphere : insights gained by combining phylogenetic and functional gene-based analyses

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Costa, Rodrigo; Gomes, Newton C. M.; Kroegerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata.

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Singh, Sunil; Gupta, Rashi; Sharma, Shilpi

2015-06-30

With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture. Copyright © 2015 Elsevier B.V. All rights reserved.

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

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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.

Rhizosphere microbial communities from resistant and susceptible watermelon cultivars showed different response to fusarium oxysporum f. sp. niveum inoculation

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Zhi, W.F.; Can, C.S.; Ling, C.; Hui, X.W.

2015-01-01

Fusarium oxysporum f. sp. niveum (FON), a soil-borne pathogen of watermelon (Citrullus lanatus), can cause substantial production losses worldwide. In this study, plate culture and PCR-denaturing gradient gel electrophoresis (DGGE) methods were used to evaluate the effects of inoculation of Fusarium oxysporum f.sp. niveum on rhizosphere microbial communities of different watermelon cultivars to FON. Two methods indicated that the effects of watermelon rhizosphere microbial community of different resistance cultivars to FON were much different. Populations of culturable bacteria and actinomycetes in the rhizosphere of susceptible watermelon cultivar were significantly lower than in the resistant cultivar after inoculation (P<0.05), but the opposite result was observed for fungi. Principal component analysis of bacterial and fungal community structure also showed that the cultivar of FON-inoculated soil treatment were separated from the non-inoculated controls after inoculation, and there was clear discrimination between the susceptible cultivars and the resistant cultivars. Sequence analysis of specific bands from DGGE profiles showed that specific rhizosphere bacterial and fungal groups differed between watermelon cultivars after inoculation . Both methods demonstrated that different resistant watermelon cultivars occupied different rhizosphere microbial communities, and and disease suppression might be correlated with high microbial diversity. F. oxysporum f. sp. Niveum alters the structure and functional diversity of microbial communities associated with watermelon rhizosphere. (author)

Interactions between selected PAHs and the microbial community in rhizosphere of a paddy soil.

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Su, Yu H; Yang, Xue Y

2009-01-15

This study investigated the interaction of three polycyclic aromatic hydrocarbons (PAHs), i.e., naphthalene (NAP), phenanthrene (PHN), and pyrene (PYR), with the microbial community in the rhizosphere of a paddy soil and the influence of the rice (Oryza sativa) rhizosphere on the microbial community structure. A range of initial NAP, PHN and PYR levels in soil (50-200, 18-72, and 6.6-26.6 mg kg(-1), respectively) were prepared and the soil samples were then aged for 4 months (to yield PAH concentrations at 1.02-1.42, 1.32-4.77, and 2.98-18.5 mg kg(-)(1), respectively) before the soil samples were planted with rice seedlings. The microbial phospholipid-fatty-acid (PLFA) patterns in PAH-contaminated soils were analyzed to elucidate the changes of the microbial biomass and community composition. Results indicated that at the applied concentrations the PAHs were not toxic to rice seedlings, as evidenced by no growth inhibition during the 8-week planting period. However, the microbial biomass, as revealed by PLFAs, decreased significantly with increasing PAH concentration in both rhizospheric and non-rhizospheric soils. The PAHs in soils were obviously toxic to microorganisms, and the toxicity of PHN was greater than PYR due likely to the higher PHN bioavailability. Total PLFAs in rhizospheric soils were profoundly higher than those in non-rhizospheric soils, suggesting that the inhibitive effect of PAHs on microbial activities was alleviated by the rice roots. The principal component analysis (PCA) of the PLFA signatures revealed pronounced changes in PLFA pattern in rhizospheric and non-rhizospheric soils with or without spiked PAHs. Using the PLFA patterns as a biomarker, it was found that Gram-positive bacteria were more sensitive to PAHs than Gram-negative bacteria, and the rhizosphere of rice roots stimulated the growth of aerobic bacteria.

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

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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.

Fate of polycyclic aromatic hydrocarbons (PAH) in the rhizosphere and myco-rhizosphere

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Leyval, C.; Beguiristain, T.; Corgie, S.; Joner, E.

2005-01-01

Organic pollutants such as polycyclic aromatic hydrocarbons (PAH) can reach high concentrations in soils due to man-made pollution related to industrial, agricultural or urban activities. Such concentrations can reach toxic values and create major environmental and health problems. One of the first entry point of pollutants in plant ecosystems is the rhizosphere, defined as the soil under the influence of roots. In the rhizosphere, the plant release root exudates, feeding soil microorganisms, and take up water and nutrients. Among the rhizosphere inhabitants, arbuscular mycorrhizal (AM) fungi are ubiquitous root symbiotic fungi, contributing to plant growth and plant nutrition. In PAH-polluted soils, biodegradation of PAH increases, which is attributed to increased microbial activity in the rhizosphere..We studied the contribution of the rhizosphere of mycorrhizal and non-mycorrhizal plants to the biodegradation of PAH in the rhizosphere, taking into account microbial community structure. Different experiments were performed with industrial contaminated soils and PAH-spiked soils, in pot cultures as well as compartmented devices allowing to analyze rhizosphere processes in consecutive sections as a function of distance to roots. Clover and ryegrass, inoculated or not with the arbuscular mycorrhizal fungus Glomus mosseae were used.. After different time periods, plants were harvested, biomass and mycorrhizal root colonization were estimated. Microbial Density of microbial heterotrophs and of degrading bacteria was estimated by MPN techniques in micro-plates. Microbial community structure was estimated by DNA extraction from the rhizosphere, amplification by PCR and analysed by TGGE (temperature gradient gel electrophoresis), or by PLFA (phospholipid fatty acid analysis). PAH in soil were extracted by Soxhlet and analysed by GC-MS. We showed that the concentration of PAH increased with the distance to roots (Corgie et al, 2003) and was lower in the myco-rhizosphere

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

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

2012-03-01

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

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

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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.

Safe-site effects on rhizosphere bacterial communities in a high-altitude alpine environment.

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Ciccazzo, Sonia; Esposito, Alfonso; Rolli, Eleonora; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

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 floristic communities rhizospheres on their soil bacterial communities.

Growth of Quailbush in Acidic, Metalliferous Desert Mine Tailings: Effect of Azospirillum brasilense Sp6 on Biomass Production and Rhizosphere Community Structure

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de-Bashan, Luz E.; Hernandez, Juan-Pablo; Nelson, Karis N.; Bashan, Yoav

2010-01-01

Mine tailing deposits in semiarid and arid environments frequently remain devoid of vegetation due to the toxicity of the substrate and the absence of a diverse soil microbial community capable of supporting seed germination and plant growth. The contribution of the plant growth promoting bacterium (PGPB) Azospirillum brasilense Sp6 to the growth of quailbush in compost-amended, moderately acidic, high-metal content mine tailings using an irrigation-based reclamation strategy was examined along with its influence on the rhizosphere bacterial community. Sp6 inoculation resulted in a significant (2.2-fold) increase in plant biomass production. The data suggest that the inoculum successfully colonized the root surface and persisted throughout the 60-day experiment in both the rhizosphere, as demonstrated by excision and sequencing of the appropriate denaturing gradient gel electrophoresis (DGGE) band, and the rhizoplane, as indicated by fluorescent in situ hybridization of root surfaces. Changes in rhizosphere community structure in response to Sp6 inoculation were evaluated after 15, 30, and 60 days using DGGE analysis of 16S rRNA polymerase chain reaction amplicons. A comparison of DGGE profiles using canonical correspondence analysis revealed a significant treatment effect (Sp6-inoculated vs. uninoculated plants vs. unplanted) on bacterial community structure at 15, 30, and 60 days (p<0.05). These data indicate that in an extremely stressed environment such as acid mine tailings, an inoculated plant growth promoting bacterium not only can persist and stimulate plant growth but also can directly or indirectly influence rhizobacterial community development. PMID:20632001

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

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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.

Soil and Cultivar Type Shape the Bacterial Community in the Potato Rhizosphere

NARCIS (Netherlands)

Inceoglu, Ozgul; Salles, Joana Falcao; van Elsas, Jan Dirk

The rhizospheres of five different potato cultivars (including a genetically modified cultivar) obtained from a loamy sand soil and two from a sandy peat soil, next to corresponding bulk soils, were studied with respect to their community structures and potential function. For the former analyses,

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.

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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

Comparison of the rhizosphere bacterial communities of Zigongdongdou soybean and a high-methionine transgenic line of this cultivar.

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Jingang Liang

Full Text Available 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.

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

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

2016-01-01

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

The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

International Nuclear Information System (INIS)

Yrjaelae, Kim; Keskinen, Anna-Kaisa; Akerman, Marja-Leena; Fortelius, Carola; Sipilae, Timo P.

2010-01-01

To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation. - The bacterial community analysis using 16S rRNA and extradiol dioxygenase marker genes in rhizoremediation revealed both a rhizosphere and a PAH-pollution effect.

Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama

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Zachary Senwo

2011-07-01

Full Text Available Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa, potato (Solanum tuberosum, onion (Allium cepa L, broccoli (Brassica oleracea var. botrytis and Tall fescue pasture grass (Festuca arundinacea. Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU at 3% dissimilarity level (roughly corresponding to the bacterial species level at 0–10 cm (581.7–770.0 compared to 10–20 cm (563.3–727.7 soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7; whereas the lowest OTUs found at 10–20 cm were under potato (563.3. The predominant phyla (85% in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria, and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more

Dynamics of Panax ginseng Rhizospheric Soil Microbial Community and Their Metabolic Function

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Yong Li

2014-01-01

Full Text Available The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD, and amplified ribosomal DNA restriction analysis (ARDRA. Culture-dependent method (Biolog was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found that Verrucomicrobia, Acidobacteria, and Proteobacteria were the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such as Pseudomonas, Burkholderia, and Bacillus, tended to be rare.

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

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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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Impacts of endophyte infection of ryegrass on rhizosphere metabolome and microbial community

DEFF Research Database (Denmark)

Wakelin, S.; Harrison, Scott James; Mander, C.

2015-01-01

37, within a genetically uniform breeding line of perennial ryegrass (Lolium perenne cv. Samson 11104) on the rhizosphere metabolome and the composition of the fungal, bacterial, and Pseudomonas communities. There were strong differences in the rhizosphere metabolomes between infested and non......-infested ryegrass strains (P=0.06). These were attributed to shifts in various n-alkane hydrocarbon compounds. The endophyte-associated alteration in rhizosphere metabolome was linked to changes in the total bacterial (P

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

Science.gov (United States)

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

Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree.

Directory of Open Access Journals (Sweden)

Abdul Latif Khan

Full Text Available Boswellia sacra, a frankincense producing endemic tree, has been well known for its cultural, religious and economic values. However, the tree has been least explored for the associated microsymbiota in the rhizosphere. The current study elucidates the fungal and bacterial communities of the rhizospheric regions of the wild and cultivated B. sacra tree populations through next generation sequencing. The sequence analysis showed the existence of 1006±8.9 and 60.6±3.1 operational taxonomic unit (OTUs for bacterial and fungal communities respectively. In fungal communities, five major phyla were found with significantly higher abundance of Ascomycota (60.3% in wild population and Basidiomycota (52% in cultivated tree rhizospheres. Among bacterial communities, 31 major phyla were found, with significant distribution of Actinobacteria in wild tree rhizospheres, whereas Proteobacteria and Acidobacteria were highly abundant in cultivated trees. The diversity and abundance of microbiome varied significantly depending upon soil characteristics of the three different populations. In addition, significantly higher glucosidases, cellulases and indole-3-acetic acid were found in cultivated tree's rhizospheres as compared to wild tree populations. for these plants to survive the harsh arid-land environmental conditions. The current study is a first comprehensive work and advances our knowledge about the core fungal and bacterial microbial microbiome associated with this economically important tree.

Cucumber rhizosphere microbial community response to biocontrol agent Bacillus subtilis B068150

Science.gov (United States)

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...

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

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Sonia Ciccazzo

2014-01-01

Full Text Available 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.

A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes.

Science.gov (United States)

Ortiz, Vilma; Phelan, Sinead; Mullins, Ewen

2016-12-01

Nematodes play a key role in soil processes with alterations in the nematode community structure having the potential to considerably influence ecosystem functioning. As a result fluctuations in nematode diversity and/or community structure can be gauged as a 'barometer' of a soil's functional biodiversity. However, a deficit exists in regards to baseline knowledge and on the impact of specific GM crops on soil nematode populations and in particular in regard to the impact of GM potatoes on the diversity of nematode populations in the rhizosphere. The goal of this project was to begin to address this knowledge gap in regards to a GM potato line, cisgenically engineered for resistance to Phytophthora infestans (responsible organism of the Irish potato famine causing late blight disease). For this, a 3 year (2013, 2014, 2015) field experimental study was completed, containing two conventional genotypes (cvs. Desiree and Sarpo Mira) and a cisgenic genotype (cv. Desiree + Rpi-vnt1). Each potato genotype was treated with different disease management strategies (weekly chemical applications and corresponding no spray control). Hence affording the opportunity to investigate the temporal impact of potato genotype, disease management strategy (and their interaction) on the potato rhizosphere nematode community. Nematode structure and diversity were measured through established indices, accounts and taxonomy with factors recording a significant effect limited to the climatic conditions across the three seasons of the study and chemical applications associated with the selected disease management strategy. Based on the metrics studied, the cultivation of the cisgenic potato genotype exerted no significant effect (P > 0.05) on nematode community diversity or structure. The disease management treatments led to a reduction of specific trophic groups (e.g. Predacious c-p = 4), which of interest appeared to be counteracted by a potato genotype with vigorous growth phenotype

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

Directory of Open Access Journals (Sweden)

Zhenping Yang

Full Text Available 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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

2014-01-01

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

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

Science.gov (United States)

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.

Analysis of bacterial and fungal community structure in replant ...

African Journals Online (AJOL)

High quality DNA is the basis of analyzing bacterial and fungal community structure in replant strawberry rhizosphere soil with the method of denaturing gradient gel electrophoresis (DGGE). DNA of soil microorganisms was extracted from the rhizosphere soil of strawberries planted in different replanted years (0, two, ...

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

Science.gov (United States)

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

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.

Science.gov (United States)

Uroz, S; Oger, P; Tisserand, E; Cébron, A; Turpault, M-P; Buée, M; De Boer, W; Leveau, J H J; Frey-Klett, P

2016-06-15

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition

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An eYang

2015-08-01

Full Text Available We evaluated effects of 9-year simulation of simulated nitrogen (N deposition on microbial composition and diversity in the rhizosphere of two dominant temperate grassland species: grass Stipa krylovii and forb Artemisia frigida. Microbiomes in S. krylovii and A.frigida rhizosphere differed, but changed consistently along the N gradient. These changes were correlated to N-induced shifts to plant community. Hence, as plant biomass changed, so did bacterial rhizosphere communities, a result consistent with the role that N fertilizer has been shown to play in altering plant-microbial mutualisms. A total of 23 bacterial phyla were detected in the two rhizospheric soils by pyrosequencing, with Proteobacteria, Acidobacteria and Bacteroidetes dominating the sequences of all samples. Bacterioidetes and Proteobacteria tended to increase, while Acidobacteria declined with increase in N addition rates. TM7 increased >5-fold in the high N addition rates, especially in S. krylovii rhizosphere. Nitrogen addition also decreased diversity of OTUs (operational taxonomic units, Shannon and Chao1 indices of rhizospheric microbes regardless of plant species. These results suggest that there were both similar but also specific changes in microbial communities of temperate steppes due to N deposition.

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

NARCIS (Netherlands)

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

The use of genetically modified (GM) plants still raises concerns about their environmental impact. The present study aimed to evaluate the possible effects of GM maize, in comparison to the parental line, on the structure and abundance of microbial communities in the rhizosphere. Moreover, the

Interactions between plant and rhizosphere microbial communities in a metalliferous soil

International Nuclear Information System (INIS)

Epelde, Lur; Becerril, Jose M.; Barrutia, Oihana; Gonzalez-Oreja, Jose A.; Garbisu, Carlos

2010-01-01

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

Interactions between plant and rhizosphere microbial communities in a metalliferous soil

Energy Technology Data Exchange (ETDEWEB)

Epelde, Lur [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Becerril, Jose M.; Barrutia, Oihana [Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P.O. Box 644, E-48080 Bilbao (Spain); Gonzalez-Oreja, Jose A. [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Garbisu, Carlos, E-mail: cgarbisu@neiker.ne [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain)

2010-05-15

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

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

Science.gov (United States)

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.

Response of archaeal communities in the rhizosphere of maize and soybean to elevated atmospheric CO2 concentrations.

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David M Nelson

Full Text Available BACKGROUND: Archaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO(2] will influence the structure and function of soil archaeal communities. METHODOLOGY/PRINCIPAL FINDINGS: We measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (∼385 ppm and elevated (550 ppm [CO(2] in a replicated and field-based study. There was no influence of elevated [CO(2] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C(4 plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C(3 plant, at elevated [CO(2], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO(2] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO(2] for soybean. CONCLUSION: Plant-driven shifts in soil biogeochemical processes in response to elevated [CO(2] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO(2] in the absence of drought.

Bacterial community structure in the Cerasus sachalinensis Kom ...

African Journals Online (AJOL)

Jane

2011-07-21

Jul 21, 2011 ... The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial ...

Composition and function of the microbial community related with the nitrogen cycling on the potato rhizosphere

International Nuclear Information System (INIS)

Florez Zapata, Nathalia; Garcia, Juan Carlos; Del Portillo, Patricia; Restrepo, Silvia; Uribe Velez, Daniel

2013-01-01

In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbial communities related with the N cycle of S. tuberosum group phureja rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy. Few significant differences between the community compositions at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population's selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil's physicalchemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

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

Science.gov (United States)

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.

Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years.

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Luo, Youfa; Wu, Yonggui; Wang, Hu; Xing, Rongrong; Zheng, Zhilin; Qiu, Jing; Yang, Lian

2018-05-01

This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag. Additionally, revegetation increased the relative abundance of plant growth-promoting rhizobacteria such as Flavobacterium, Streptomyces, and Arthrobacter as well as symbiotic N 2 fixers such as Bradyrhizobium. Three dominant native plant species (Arundo donax, Broussonetia papyrifera, and Robinia pseudoacacia) greatly increased the quality of the rhizosphere slags. Canonical correspondence analysis showed that the differences in bacterial community structure between the bulk and rhizosphere slags were explained by slag properties, i.e., pH, available copper (Cu) and lead (Pb), moisture, available nitrogen (N), phosphorus (P), and potassium (K), and organic matter (OM); however, available Zn and cadmium (Cd) contents were the slag parameters that best explained the differences between the rhizosphere communities of the eight plant species. The results suggested that revegetation plays an important role in enhancing bacterial community abundance and diversity in rhizosphere slags and that revegetation may also regulate microbiological properties and diversity mainly through changes in heavy metal bioavailability and physiochemical slag characteristics.

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

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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.

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.

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Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

2016-12-06

Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.

COMPOSITION AND FUNCTION OF THE MICROBIAL COMMUNITY RELATED WITH THE NITROGEN CYCLING ON THE POTATO RHIZOSPHERE

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Nathalia Maria Vanesa Florez Zapata

2013-09-01

Full Text Available In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants’ nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbal[trm1]  communities related with the N cycle of S. tuberosum group phureja  rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy.  Few significant differences between the community composition at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population’s selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas, appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil’s physical-chemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community.

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Soumitra Paul Chowdhury

Full Text Available 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.

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

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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.

[Effects of wheat root exudates on cucumber growth and soil fungal community structure].

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Wu, Feng-Zhi; Li, Min; Cao, Peng; Ma, Ya-Fei; Wang, Li-Li

2014-10-01

With wheat as the donor plant and cucumber as the receptor plant, this study investigated the effects of root exudates from wheat cultivars with different allelopathic potentials (positive or negative) and companion cropping with wheat on soil fungal community structure by PCR-DGGE method and cucumber growth. Results showed that the wheat root exudates with positive allelopathic potential increased height and stem diameter of cucumber seedlings significantly, compared to the control seedlings (W) after 6 days and 12 days treatment, respectively. Also, wheat root exudates with both positive and negative allelopathic potential increased the seedling height of cucumber significantly after 18 days treatment. The wheat root exudates with different allelopathic potentials decreased the band number, Shannon and evenness indices of soil fungal community significantly in cucumber seedling rhizosphere, and those in the soil with the control seedlings (W) were also significantly higher than that in the control soil without seedlings (Wn) after 6 days treatment. The band number, Shannon and evenness indices in all the treatments were significantly higher than those in the control soil without seedlings (Wn) after 18 days treatment. Companion cropping with negative allelopathic potential wheat decreased the Shannon and evenness indices of soil fungi community significantly in the cucumber seedling rhizosphere, suggesting the wheat root exudates and companion cropping with wheat changed soil fungal community structure in the cucumber seedling rhizosphere. The results of DGGE map and the principal component analysis showed that companion cropping with wheat cultivars with different allelopathic potentials changed soil fungal community structure in cucumber seedling rhizosphere.

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

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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.

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

KAUST Repository

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

2018-01-01

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.

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

KAUST Repository

Mapelli, Francesca

2018-01-09

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.

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

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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 (pfertilized plants. Plant anatomy, and other factors related to field location, possibly associated with edaphic and air characteristics, were more influential drivers of different tomato organ microbiomes than were diverse soil amendment applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Insights into the Regulation of Rhizosphere Bacterial Communities by Application of Bio-organic Fertilizer in Pseudostellaria heterophylla Monoculture Regime

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Linkun Wu

2016-11-01

Full Text Available The biomass and quality of Pseudostellariae heterophylla suffers a significant decline under monoculture. Since rhizosphere microbiome plays crucial roles in soil health, deep pyrosequencing combined with qPCR was applied to characterize the composition and structure of soil bacterial community under monoculture and different amendments. The results showed compared with the first-year planted (FP, second-year monoculture of P. heterophylla (SP led to a significant decline in yield and resulted in a significant increase in Fusarium oxysporum but a decline in Burkholderia spp. Bio-organic fertilizer (MT formulated by combining antagonistic bacteria with organic matter could significantly promote the yield by regulating rhizosphere bacterial community. However, organic fertilizer (MO without antagonistic bacteria could not suppress Fusarium wilt. Multivariate statistics analysis showed a distinct separation between the healthy samples (FP and MT and the unhealthy samples (SP and MO, suggesting a strong relationship between soil microbial community and plant performance. Furthermore, we found the application of bio-organic fertilizer MT could significantly increase the bacterial community diversity and restructure microbial community with relatively fewer pathogenic F. oxysporum and more beneficial Burkholderia spp. In conclusion, the application of novel bio-organic fertilizer could effectively suppress Fusarium wilt by enriching the antagonistic bacteria and enhancing the bacterial diversity.

Proliferation of the biocontrol agent Fusarium oxysporum f. sp. strigae and its impact on indigenous rhizosphere fungal communities in maize under different agro-ecologies.

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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.

Bacterial communities in the rhizosphere of amilaceous maize (Zea mays L. as assessed by pyrosequencing

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David Correa-Galeote

2016-07-01

Full Text Available 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

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

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Yuxuan Qin

2017-12-01

Full Text Available 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.

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

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

2014-02-01

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.

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

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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

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Susanne eSchreiter

2014-04-01

Full Text Available 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 ten 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 three and seven 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 different soils. The number of rhizosphere responders was highest three 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.

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

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Rajal Debnath

2016-09-01

Full Text Available Information on rhizosphere micobiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant R. 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 (3912m 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.

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

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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.

Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

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Yang SONG,Chen ZHU,Waseem RAZA,Dongsheng WANG,Qiwei HUANG,Shiwei GUO,Ning LING,Qirong SHEN

2016-09-01

Full Text Available Grafting is commonly used to overcome soil-borne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper, significant negative correlations between the bacterial alpha diversity and both the disease incidence (r = -0.832, P = 0.005 and pathogen population (r = - 0.786, P = 0.012 were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure (beta diversity in the rhizosphere. Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.

Influence of humic substances on plant-microbes interactions in the rhizosphere

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Puglisi, Edoardo; Pascazio, Silvia; Spaccini, Riccardo; Crecchio, Carmine; Trevisan, Marco; Piccolo, Alessandro

2013-04-01

Humic substances are known to play a wide range of effects on the physiology of plant and microbes. This is of particular relevance in the rhizosphere of terrestrial environments, where the reciprocal interactions between plants roots, soil constituents and microorganisms strongly influence the plants acquisition of nutrients. Chemical advances are constantly improving our knowledge on humic substances: their supra-molecular architecture, as well as the moltitude of their chemical constituents, many of which are biologically active. An approach for linking the structure of humic substances with their biological activity in the rhizosphere is the use of rhizoboxes, which allow applying a treatment (e.g., an amendment with humic substances) in an upper soil-plant compartment and take measurements in a lower isolated rhizosphere compartment that can be sampled at desired distances from the rhizoplane. This approach can be adopted to assess the effects of several humic substances, as well as composted materials, on maize plants rhizodeposition of carbon, and in turn on the structure and activity of rhizosphere microbial communities. In order to gain a complete understanding of processes occurring in the complex soil-plant-microorganisms tripartite system, rhizobox experiments can be coupled with bacterial biosensors for the detection and quantification of bioavailable nutrients, chemical analyses of main rhizodeposits constituents, advanced chemical characterizations of humic substances, DNA-fingerprinting of microbial communities, and multivariate statistical approaches to manage the dataset produced and to infer general conclusions. By such an approach it was found that humic substances are significantly affecting the amount of carbon deposited by plant roots. This induction effect is more evident for substances with more hydrophobic and complex structure, thus supporting the scientific hypothesis of the "microbial loop model", which assumes that plants feed

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

OpenAIRE

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 ph...

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

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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

Impacts of fertilization regimes on arbuscular mycorrhizal fungal (AMF community composition were correlated with organic matter composition in maize rhizosphere soil

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Chen Zhu

2016-11-01

Full Text Available 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 analysed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three 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 AMF community

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

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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.

Growth rates of rhizosphere microorganisms depend on competitive abilities of plants for nitrogen

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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

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce.

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Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

2016-04-28

Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3(-)-N, and NH4(+)-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce

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Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

2016-04-01

Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3--N, and NH4+-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea and Its Rhizospheric Microbial Communities--A Comparison between Chemical Fertilizers and Bioinoculants.

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Rashi Gupta

Full Text Available 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.

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

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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 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.

Understanding Aquatic Rhizosphere Processes Through Metabolomics and Metagenomics Approach

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

2013-04-01

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

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

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Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

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

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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.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

International Nuclear Information System (INIS)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir; He Yan; Xu Jianming

2010-01-01

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

Energy Technology Data Exchange (ETDEWEB)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); He Yan, E-mail: yhe2006@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); Xu Jianming, E-mail: jmxu@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China)

2010-08-15

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

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

Science.gov (United States)

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

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

Science.gov (United States)

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

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Jirong Wu

Full Text Available 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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

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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.

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

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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

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

NARCIS (Netherlands)

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

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 beta-propeller phytases (BPP) in the rhizosphere of traditional and transgenic maize

Salicornia strobilacea (synonym of Halocnemum strobilaceum) Grown Under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

KAUST Repository

Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira Santillá n, Marí a José ; Fusi, Marco; Bariselli, Paola; Reddy, Muppala P.; 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 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.

Salicornia strobilacea (synonym of Halocnemum strobilaceum) Grown Under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

KAUST Repository

Marasco, Ramona

2016-04-01

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 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.

Is rhizosphere remediation sufficient for sustainable revegetation of mine tailings?

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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

Is rhizosphere remediation sufficient for sustainable revegetation of mine tailings?

Science.gov (United States)

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

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

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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 (Psoil 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 effective at enhancing microbial N mineralization under organically managed soils. Thus, to optimize crop N availability from organic sources, breeding efforts

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

Science.gov (United States)

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

Fungi isolated from the rhizosphere of spring cruciferous plants

Directory of Open Access Journals (Sweden)

Barbara Majchrzak

2013-12-01

Full Text Available Fungal communities isolated from the rhizosphere of spring cruciferous plants were analysed in the study. It was found that the rhizosphere of crucifers was colonized primarily by fungi of the order Mucorales and of the genus Fusarium. Members of the genus Fusarium dominated in the rhizoplane. The roots of cruciferous plants secrete glucosinolates – secondary metabolites known for their antifungal properties, thus affecting the communities of soil-dwelling fungi.

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

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Wietse de Boer

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

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

Science.gov (United States)

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

Rhizosphere Protists Change Metabolite Profiles in Zea mays

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Anke Kuppardt

2018-05-01

Full Text Available 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.

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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.

[Effects of short-term elevated CO2 concentration and drought stress on the rhizosphere effects of soil carbon, nitrogen and microbes of Bothriochloa ischaemum.

Science.gov (United States)

Xiao, Lie; Liu, Guo Bin; Li, Peng; Xue, Sha

2017-10-01

A water control pot experiment was conducted in climate controlled chambers to study soil carbon, nitrogen and microbial community structure and their rhizosphere effects in the rhizosphere and non rhizosphere soil of Bothriochloa ischaemum at elevated CO2 concentrations (800 μmol·mol -1 ) under three water regimes, i.e., well watered (75%-80% of field capacity, FC), moderate drought stress (55%-60% of FC), and severe drought stress (35%-40% of FC). The results showed that elevated CO2 concentration and drought stress did not have significant impacts on the content of soil organic carbon, total nitrogen or dissolved organic carbon (DOC) in the rhizosphere and bulk soils or their rhizosphere effects. Elevated CO2 concentration significantly decreased dissolved organic nitrogen (DON) content in the rhizosphere soil under moderate drought stress, increased DOC/DON, and significantly increased the negative rhizosphere effect of DON and positive rhizosphere effect of DOC/DON. Drought stress and elevated CO2 concentration did not have significant impacts on the rhizosphere effect of total and bacterial phospholipid fatty acids (PLFA). Drought stress under elevated CO2 concentration significantly increased the G + /G - PLFA in the rhizosphere soil and decreased the G + /G - PLFA in the bulk soil, so its rhizosphere effect significantly increased, indicating that the soil microbial community changed from chemoautotroph microbes to heterotrophic microbes.

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

Science.gov (United States)

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.

Salicornia strobilacea (synonym of Halocnemum strobilaceum Grown Under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

Directory of Open Access Journals (Sweden)

Ramona Marasco

2016-08-01

Full Text Available 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 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.

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

Science.gov (United States)

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.

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

KAUST Repository

Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J.; Fusi, Marco; Bariselli, Paola; Reddy, Muppala P.; 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.

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

KAUST Repository

Marasco, Ramona

2016-08-22

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.

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

Science.gov (United States)

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.

Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology

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Peer M. Schenk

2013-08-01

Full Text Available Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling.

Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress.

Science.gov (United States)

Bharti, Nidhi; Barnawal, Deepti; Maji, Deepamala; Kalra, Alok

2015-07-01

The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities.

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality

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Linlin Dong

2018-03-01

Full Text Available The cultivation of Panax plants is hindered by replanting problems, which may be caused by plant-driven changes in the soil microbial community. Inoculation with microbial antagonists may efficiently alleviate replanting issues. Through high-throughput sequencing, this study revealed that bacterial diversity decreased, whereas fungal diversity increased, in the rhizosphere soils of adult ginseng plants at the root growth stage under different ages. Few microbial community, such as Luteolibacter, Cytophagaceae, Luteibacter, Sphingomonas, Sphingomonadaceae, and Zygomycota, were observed; the relative abundance of microorganisms, namely, Brevundimonas, Enterobacteriaceae, Pandoraea, Cantharellales, Dendryphion, Fusarium, and Chytridiomycota, increased in the soils of adult ginseng plants compared with those in the soils of 2-year-old seedlings. Bacillus subtilis 50-1, a microbial antagonist against the pathogenic Fusarium oxysporum, was isolated through a dual culture technique. These bacteria acted with a biocontrol efficacy of 67.8%. The ginseng death rate and Fusarium abundance decreased by 63.3% and 46.1%, respectively, after inoculation with B. subtilis 50-1. Data revealed that microecological degradation could result from ginseng-driven changes in rhizospheric microbial communities; these changes are associated with the different ages and developmental stages of ginseng plants. Biocontrol using microbial antagonists alleviated the replanting problem. KEY WORDS: Panax ginseng, Microbial communities, Replanting problem, High-throughput sequencing, Different ages, Bioremediation

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

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Amélia Bourceret

Full Text Available 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.

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites

Energy Technology Data Exchange (ETDEWEB)

Elhottova, D.; Kristufek, V.; Maly, S.; Frouz, J. [Academy of Sciences of the Czech Republic, Ceske Budejovice (Czech Republic). Inst. for Soil Biology

2009-07-01

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm{sup 3} of tertiary alkaline clay sediment from Sokolov brown-coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential in comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N{sub 2}) fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara.

Functional patterns of microbial communities of rhizospheric soils across the development stages of a young mangrove in French Guiana.

Science.gov (United States)

Luglia, Mathieu; Criquet, Stéven; Sarrazin, Max; Ziarelli, Fabio; Guiral, Daniel

2014-02-01

The functional patterns of microbial communities (microbial respiration, enzyme activities, functional diversity) and the relevant physico-chemical characteristics of rhizospheric soils were studied during the process of mudflat colonization by mangrove. The study site is a fringe mangrove stand located in Montabo Bay at Cayenne (French Guiana). It is characterized by different vegetation development stages dominated by an assemblage of Avicennia germinans and Laguncularia racemosa. Rhizospheric and surface soils were collected from three stations based on successional stages of mangrove colonization: pioneer (P), coppice (C), and young forest (F). The microbial functional patterns showed significant progressive shifts along the mangrove vegetation profile. The P stages, those most influenced by tide currents, were macroscopically characterized by hydro-sedimentary instability and micro-phytobenthic colonization of mudflat. This stage, characterized by low total organic carbon (TOC) content and quality, showed the lowest extracellular enzymatic activities and the highest functional metabolic diversities. TOC quality analyses by (13)C CPMAS NMR provided evidence of progressive TOC enrichment and an increasing imprint of aboveground vegetation on C quality as succession occurs. These differences in the origin, amount, and quality of soil organic matter (SOM) of older stages exerted both a quantitative and qualitative control over microbial functional responses. This indicated the enhancement of aboveground-belowground functional linkages, leading to the expression of high decomposition activities and a functional loss and specialization of rhizospheric microbial communities.

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

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Wei Hui Xu

2015-09-01

Full Text Available 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.

Comparisons of Soil Properties, Enzyme Activities and Microbial Communities in Heavy Metal Contaminated Bulk and Rhizosphere Soils of Robinia pseudoacacia L. in the Northern Foot of Qinling Mountain

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Yurong Yang

2017-11-01

Full Text Available The toxic effects of heavy metal (HM contamination on plant metabolism and soil microorganisms have been emphasized recently; however, little is known about the differences in soil physical, chemical, and biological properties between bulk and rhizosphere soils contaminated with HMs in forest ecosystem. The present study was conducted to evaluate the rhizosphere effect on soil properties, enzyme activities and bacterial communities associated with Robinia pseudoacacia L. along a HM contamination gradient. Soil organic matter (SOM, available nitrogen (AN and phosphorus (AP contents were significantly higher in rhizosphere soil than those in bulk soil at HM contaminated sites (p < 0.05. Compared to bulk soil, activities of four soil enzymes indicative of C cycle (β-glucosidase, N cycle (protease, urease and P cycle (alkaline phosphatase in rhizosphere soil across all study sites increased by 47.5%, 64.1%, 52.9% and 103.8%, respectively. Quantitative PCR (qPCR and restriction fragment length polymorphism (RFLP were used to determine the relative abundance, composition and diversity of bacteria in both bulk and rhizosphere soils, respectively. The copy number of bacterial 16S rRNA gene in bulk soil was significantly lower than that in rhizosphere soil (p < 0.05, and it had significantly negative correlations with total/DTPA-extractable Pb concentrations (p < 0.01. Alphaproteobacteria, Gammaproteobacteria and Firmicutes were the most dominant groups of bacteria at different study sites. The bacterial diversity index of Species richness (S and Margalef (dMa were significantly higher in rhizosphere soil compared with those in bulk soil, although no difference could be found in Simpson index (D between bulk and rhizosphere soils (p > 0.05. Redundancy analysis (RDA results showed that soil pH, EC, SOM and total/DTPA-extractable Pb concentrations were the most important variables affecting relative abundance, composition and diversity of bacteria (p < 0

Pesticide dissipation and microbial community changes in a biopurification system: influence of the rhizosphere.

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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.

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

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Ying Nie

2016-01-01

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

Microbial based strategies for assessing rhizosphere-enhanced phytoremediation

Energy Technology Data Exchange (ETDEWEB)

Reynolds, C M [US Army Cold Regions Research and Engineering Lab., Hanover, NH (United States); Wolf, D C [Arkansas Univ., Fayetteville, AR (United States)

1999-01-01

The U.S. Department of Defense has considered phytoremediation to be a feasible technology to clean up contaminated sites in remote, cold regions. In cold regions, contaminated soil treatment rates are reduced by low temperatures and short treatment seasons. One technology that overcomes these limitations is rhizosphere-enhanced biotreatment which is a low-cost, simple technology that stimulates indigenous microorganisms. A study was conducted in which rhizosphere-enhanced treatment was compared to natural attenuation at a petroleum-contaminated site in Fairbanks, Alaska. The effects of vegetation and nutrient additions on remediation of soils contaminated with both diesel and crude oil were examined. Soil total petroleum hydrocarbon (TPH) concentrations in both treatments decreased relative to the initial TPH concentrations. After 640 days of treatment, the rhizosphere treatment had significantly lower TPH concentrations. It was concluded that an improved understanding of the time-dependent relationships between contaminant concentration changes and microbial community changes, along with improved techniques to characterize microbial communities, could provide a useful tool for monitoring the functioning of phytoremediation. 25 refs., 8 figs.

Microbial based strategies for assessing rhizosphere-enhanced phytoremediation

International Nuclear Information System (INIS)

Reynolds, C.M.; Wolf, D.C.

1999-01-01

The U.S. Department of Defense has considered phytoremediation to be a feasible technology to clean up contaminated sites in remote, cold regions. In cold regions, contaminated soil treatment rates are reduced by low temperatures and short treatment seasons. One technology that overcomes these limitations is rhizosphere-enhanced biotreatment which is a low-cost, simple technology that stimulates indigenous microorganisms. A study was conducted in which rhizosphere-enhanced treatment was compared to natural attenuation at a petroleum-contaminated site in Fairbanks, Alaska. The effects of vegetation and nutrient additions on remediation of soils contaminated with both diesel and crude oil were examined. Soil total petroleum hydrocarbon (TPH) concentrations in both treatments decreased relative to the initial TPH concentrations. After 640 days of treatment, the rhizosphere treatment had significantly lower TPH concentrations. It was concluded that an improved understanding of the time-dependent relationships between contaminant concentration changes and microbial community changes, along with improved techniques to characterize microbial communities, could provide a useful tool for monitoring the functioning of phytoremediation. 25 refs., 8 figs

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

Energy Technology Data Exchange (ETDEWEB)

Allen White, Richard; Borkum, Mark I.; Rivas-Ubach, Albert; Bilbao, Aivett; Wendler, Jason P.; Colby, Sean M.; Köberl, Martina; Jansson, Christer

2017-06-01

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.

Influence of introduced potential biocontrol agents on maize seedling growth and bacterial community structure in the rhizosphere

NARCIS (Netherlands)

Kozdroj, J; Trevors, JT; van Elsas, JD

Two species of Pseudomonas chromosomally tagged with gfp, which had shown antagonistic activity against the tomato pathogen Ralstonia solanacearum in a previous study, were assessed for their impact in the rhizosphere of maize. Plant growth characteristics, numbers of indigenous heterotrophic

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

Science.gov (United States)

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...

Antifungal rhizosphere bacteria can increase as response to the presence of saprotrophic fungi

NARCIS (Netherlands)

Boer, de W.; Hundscheid, M.P.J.; Klein Gunnewiek, P.J.A.; Ridder-Duine, De A.S.; Thion, C.; Veen, van J.A.; Wal, van der Annemieke

2015-01-01

Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere

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

KAUST Repository

Alzubaidy, Hanin S.

2015-11-10

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

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

Science.gov (United States)

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.

Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site.

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Jian Sun

Full Text Available We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant and a new planting site (NewPlant in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil and from the new planting site (NewSoil was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant. More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria. The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.

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

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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.

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

Science.gov (United States)

Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

2015-09-01

Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

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

Science.gov (United States)

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

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere.

Science.gov (United States)

Essarioui, Adil; LeBlanc, Nicholas; Kistler, Harold C; Kinkel, Linda L

2017-07-01

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 work, we characterized antagonistic activities and nutrient use among Streptomyces and Fusarium from the rhizosphere of Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants growing in communities of 1 (monoculture) or 16 (polyculture) plant species. Streptomyces from monoculture were more antagonistic against Fusarium than those from polyculture. In contrast, Fusarium isolates from polyculture had greater inhibitory capacities against Streptomyces than isolates from monoculture. Although Fusarium isolates had on average greater niche widths, the collection of Streptomyces isolates in total used a greater diversity of nutrients for growth. Plant richness, but not plant host, influenced the potential for resource competition between the two taxa. Fusarium isolates had greater niche overlap with Streptomyces in monoculture than polyculture, suggesting greater potential for Fusarium to competitively challenge Streptomyces in monoculture plant communities. In contrast, Streptomyces had greater niche overlap with Fusarium in polyculture than monoculture, suggesting that Fusarium experiences greater resource competition with Streptomyces in polyculture than monoculture. These patterns of competitive and inhibitory phenotypes among Streptomyces and Fusarium populations are consistent with selection for Fusarium-antagonistic Streptomyces populations in the presence of strong Fusarium resource competition in plant monocultures. Similarly, these results suggest selection for Streptomyces-inhibitory Fusarium populations in the presence of strong Streptomyces resource competition in more diverse plant communities. Thus, landscape-scale variation in plant species richness may be

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

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Bo eYang

2015-09-01

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

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

Science.gov (United States)

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.

Effects of Plant Genotype and Growth Stage on the Betaproteobacterial Communities Associated with Different Potato Cultivars in Two Fields

NARCIS (Netherlands)

Inceoglu, O.; Salles, J.F.; Overbeek, van L.S.; Elsas, van J.D.

2010-01-01

Bacterial communities in the rhizosphere are dynamic and susceptible to changes in plant conditions. Among the bacteria, the betaproteobacteria play key roles in nutrient cycling and plant growth promotion, and hence the dynamics of their community structures in the rhizosphere should be

Exploration of hitherto-uncultured bacteria from the rhizosphere

NARCIS (Netherlands)

Rocha, da U.N.; Overbeek, van L.S.; Elsas, van J.D.

2009-01-01

The rhizosphere environment selects a particular microbial community that arises from the one present in bulk soil due to the release of particular compounds in exudates and different opportunities for microbial colonization. During plant-microorganism coevolution, microbial functions supporting

Exploration of hitherto-uncultured bacteria from the rhizosphere

NARCIS (Netherlands)

da Rocha, Ulisses Nunes; van Overbeek, Leo; van Elsas, Jan Dirk

The rhizosphere environment selects a particular microbial community that arises from the one present in bulk soil due to the release of particular compounds in exudates and different opportunities for microbial colonization. During plant-microorganism coevolution, microbial functions supporting

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Giorgia Novello

2017-08-01

Full Text Available 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.

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke

Science.gov (United States)

Yang, Hui; Hu, Jinxiang; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

2016-02-01

The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0-20 cm soil layer vertically and 0-30 cm horizontally from the plant centre. Root concentrations of K+, Na+, Mg2+ and particularly Ca2+ were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0-5 cm and 5-10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities.

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

Science.gov (United States)

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

2014-03-01

The rhizosphere effect of a special phytoremediating species known as Fire Phoenix on the degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated, including changes of the enzymatic activity and microbial communities in rhizosphere soil. The study showed that the degradation rate of Σ8PAHs by Fire Phoenix was up to 99.40% after a 150-day culture. The activity of dehydrogenase (DHO), peroxidase (POD) and catalase (CAT) increased greatly, especially after a 60-day culture, followed by a gradual reduction with an increase in the planting time. The activity of these enzymes was strongly correlated to the higher degradation performance of Fire Phoenix growing in PAH-contaminated soils, although it was also affected by the basic characteristics of the plant species itself, such as the excessive, fibrous root systems, strong disease resistance, drought resistance, heat resistance, and resistance to barren soil. The activity of polyphenoloxidase (PPO) decreased during the whole growing period in this study, and the degradation rate of Σ8PAHs in the rhizosphere soil after having planted Fire Phoenix plants had a significant (R(2)=0.947) negative correlation with the change in the activity of PPO. Using an analysis of the microbial communities, the results indicated that the structure of microorganisms in the rhizosphere soil could be changed by planting Fire Phoenix plants, namely, there was an increase in microbial diversity compared with the unplanted soil. In addition, the primary advantage of Fire Phoenix was to promote the growth of flora genus Gordonia sp. as the major bacteria that can effectively degrade PAHs. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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.

Light structures phototroph, bacterial and fungal communities at the soil surface.

Directory of Open Access Journals (Sweden)

Lawrence O Davies

Full Text Available The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm and bulk soil (3-12 mm using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans

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Sayak Ganguli

2017-12-01

Full Text Available This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern Acrostichum aureum Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3–V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked reads were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes. The data is available at the NCBI - Sequence Read Archive with accession number: SRX2660456. This is the first report of the rhizospheric microbiome belonging to a fern species.

rhizosphere and non-rhizosphere soil mycoflora of corchorus olitorius

African Journals Online (AJOL)

Olahan et. al

11.24% (percentage moisture content), 0.29ml/g (water holding ... into two types, namely rhizosphere soil and non-rhizosphere soil. ... α-tocopherol equivalent to vitamin E (Oyedele et al., 2006). The ... Ilorin and stored in a sterile polythene bag prior to use. ... Organic matter content, texture and water holding capacity of soil.

Effects of field-grown genetically modified Zoysia grass on bacterial community structure.

Science.gov (United States)

Lee, Yong-Eok; Yang, Sang-Hwan; Bae, Tae-Woong; Kang, Hong-Gyu; Lim, Pyung-Ok; Lee, Hyo-Yeon

2011-04-01

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P〈0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

Biodegradation of polycyclic aromatic hydrocarbons, selection and dynamics of bacterial populations in the rhizosphere in relation with the distance to roots; Biodegradation des Hydrocarbures Aromatiques Polycycliques, selection et dynamique des populations bacteriennes dans la rhizosphere en fonction de la distance aux racines

Energy Technology Data Exchange (ETDEWEB)

Corgie, St.

2004-03-01

The biodegradation of Polycyclic Aromatic Hydrocarbons (PAH) is mainly performed by microorganisms that can use these compounds as sole source of carbon and energy. Such capacity has been amply studied to use and optimise microbial activity for remediation of contaminated soils. The use of plants has been suggested to increase and accelerate biodegradation rate by improving microbial activity. However, biodegradation mechanisms still remain poorly described as the interactions between plant, pollutant and rhizosphere microflora are often complex. A simplified compartmented device was developed to study rhizospheric processes, especially biodegradation of PAH, as a function of distance to roots, where root exudates and/or PAH were the only carbon sources for microbial growth. The development and use of bio-molecular techniques (nucleic acid isolation, PCR, RT-PCR, TGGE, hybridization with a degradation gene specific probe) permitted to follow the structure of bacterial communities. Gradients of phenanthrene biodegradation were observed as a function of distance to roots, in parallel to spatial and temporal variations in bacterial community structure. These bacterial communities, as well as PAH biodegradation rate, also depended on the aromaticity of PAH and were modified by the symbiosis between plant and an arbuscular mycorrhizal fungus. (author)

Ammonia-oxidizing Bacteria and Archaea in the Rhizosphere of Freshwater Macrophytes

DEFF Research Database (Denmark)

Herrmann, Martina; Schramm, Andreas

2007-01-01

AMMONIA-OXIDIZING ARCHAEA AND BACTERIA IN THE RHIZOSPHERE OF FRESHWATER MACROPHYTES Martina Herrmann and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia dortmanna release oxygen from...... their roots and thereby stimulate nitrification and coupled nitrification-denitrification in their rhizosphere. However, oxygen release and inorganic nitrogen concentrations differ markedly between macrophyte species. We therefore propose (i) that the rhizosphere of freshwater macrophytes harbours a species......-specific microbial community distinct from that of unvegetated sediment and (ii) that aquatic macrophytes have an impact on abundance and activity of nitrifying and denitrifying bacteria in freshwater sediment. The goal of this study was to test these hypotheses for the key functional group for coupled nitrification...

Rhizosphere priming: a nutrient perspective

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Feike Auke Dijkstra

2013-07-01

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

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

Science.gov (United States)

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 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 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.

The Date Palm Tree Rhizosphere Is a Niche for Plant Growth Promoting Bacteria in the Oasis Ecosystem

Directory of Open Access Journals (Sweden)

Raoudha Ferjani

2015-01-01

Full Text Available In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i the driving forces determining the shape of root-associated bacterial communities and (ii the plant growth promoting (PGP services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

The Date Palm Tree Rhizosphere Is a Niche for Plant Growth Promoting Bacteria in the Oasis Ecosystem

KAUST Repository

Ferjani, Raoudha

2015-04-01

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

The Date Palm Tree Rhizosphere Is a Niche for Plant Growth Promoting Bacteria in the Oasis Ecosystem

KAUST Repository

Ferjani, Raoudha; Marasco, Ramona; Rolli, Eleonora; Cherif, Hanene; Cherif, Ameur; Gtari, Maher; Boudabous, Abdellatif; Daffonchio, Daniele; Ouzari, Hadda-Imene

2015-01-01

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

Bacterial community structure in the Cerasus sachalinensis Kom ...

African Journals Online (AJOL)

The results showed that the bacterial community diversity in the cultivated C. sachalinensis rhizosphere was always higher than the wild, while the evenness and dominance indices followed a different pattern as compared to band richness in the wild and cultivated conditions. The plant growth stages also had an influence ...

Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils.

Science.gov (United States)

Cébron, Aurélie; Beguiristain, Thierry; Bongoua-Devisme, Jeanne; Denonfoux, Jérémie; Faure, Pierre; Lorgeoux, Catherine; Ouvrard, Stéphanie; Parisot, Nicolas; Peyret, Pierre; Leyval, Corinne

2015-09-01

The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the

Impact of selection on maize root traits and rhizosphere interactions

Science.gov (United States)

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.

Microinvertebrates in CELSS Hydroponic Rhizosphere: Experimental Invasion as a Test of Community Stability and a Test of a Method to Measure Bacterivory

Science.gov (United States)

Sager, John; Garland, Jay; Jenkins, David G.

1996-01-01

This report consists of two separate draft manuscripts, each prepared for submittal to a peer-reviewed journal after Kennedy Space Center (KSC) colleague editorial review and final revision. References for the two papers have been combined in this report. The two manuscripts are: (1) Experimental invasion of aquatic rhizosphere habitat and invertebrate communities, and (2) Lysozyme analysis is neither protistan- or bacteriore-specific.

Rhizosphere size

Science.gov (United States)

Kuzyakov, Yakov; Razavi, Bahar

2017-04-01

Estimation of the soil volume affected by roots - the rhizosphere - is crucial to assess the effects of plants on properties and processes in soils and dynamics of nutrients, water, microorganisms and soil organic matter. The challenges to assess the rhizosphere size are: 1) the continuum of properties between the root surface and root-free soil, 2) differences in the distributions of various properties (carbon, microorganisms and their activities, various nutrients, enzymes, etc.) along and across the roots, 3) temporal changes of properties and processes. Thus, to describe the rhizosphere size and root effects, a holistic approach is necessary. We collected literature and own data on the rhizosphere gradients of a broad range of physico-chemical and biological properties: pH, CO2, oxygen, redox potential, water uptake, various nutrients (C, N, P, K, Ca, Mg, Mn and Fe), organic compounds (glucose, carboxylic acids, amino acids), activities of enzymes of C, N, P and S cycles. The collected data were obtained based on the destructive approaches (thin layer slicing), rhizotron studies and in situ visualization techniques: optodes, zymography, sensitive gels, 14C and neutron imaging. The root effects were pronounced from less than 0.5 mm (nutrients with slow diffusion) up to more than 50 mm (for gases). However, the most common effects were between 1 - 10 mm. Sharp gradients (e.g. for P, carboxylic acids, enzyme activities) allowed to calculate clear rhizosphere boundaries and so, the soil volume affected by roots. The first analyses were done to assess the effects of soil texture and moisture as well as root system and age on these gradients. The most properties can be described by two curve types: exponential saturation and S curve, each with increasing and decreasing concentration profiles from the root surface. The gradient based distribution functions were calculated and used to extrapolate on the whole soil depending on the root density and rooting intensity. We

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-06-01

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. The 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.

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

Science.gov (United States)

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

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities.

Science.gov (United States)

Iffis, Bachir; St-Arnaud, Marc; Hijri, Mohamed

2017-01-01

Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species ( Solidago canadensis, Populus balsamifera , and Lycopus europaeus ) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities

Directory of Open Access Journals (Sweden)

Bachir Iffis

2017-08-01

Full Text Available Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities

Science.gov (United States)

Iffis, Bachir; St-Arnaud, Marc; Hijri, Mohamed

2017-01-01

Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the

Impact of plant domestication on rhizosphere microbiome assembly and functions

NARCIS (Netherlands)

Perez Jaramillo, Juan Esteban; Mendes, Rodrigo; Raaijmakers, Jos

2016-01-01

The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the

Stimulation of bacteria and protists in rhizosphere of glyphosate-treated barley

DEFF Research Database (Denmark)

Imparato, Valentina; Santos, Susana; Johansen, Anders

2016-01-01

and protist communities to foliar application of glyphosate, we measured bacterial and protist abundance, diversity and physiological status, as well as soil organic carbon. Foliar application of glyphosate doubled bacterial abundance of the culturable fraction present in the rhizosphere compared to the other...... treatments with no effect on total abundance. Also the abundance of culturable protists increased as an effect of glyphosate and the bacterial genetic diversity as revealed by 16S rDNA DGGE analysis was affected. Overall, the results indicate that when barley leaves are treated with glyphosate......, the availability of organic carbon in the rhizosphere of the dying roots is altered, which in turn may alter the bacterial and protist communities and their interactions. This can have implications for general soil carbon turnover processes and CO2 release in arable systems....

Effect of Elodea nuttallii roots on bacterial communities and MMHg proportion in a Hg polluted sediment.

Science.gov (United States)

Regier, Nicole; Frey, Beat; Converse, Brandon; Roden, Eric; Grosse-Honebrink, Alexander; Bravo, Andrea Garcia; Cosio, Claudia

2012-01-01

The objective of this study was to assess the effect of a rooted macrophyte Elodea nuttallii on rhizosphere bacterial communities in Hg contaminated sediments. Specimens of E. nuttallii were exposed to sediments from the Hg contaminated Babeni reservoir (Olt River, Romania) in our microcosm. Plants were allowed to grow for two months until they occupied the entirety of the sediments. Total Hg and MMHg were analysed in sediments where an increased MMHg percentage of the total Hg in pore water of rhizosphere sediments was found. E. nuttallii roots also significantly changed the bacterial community structure in rhizosphere sediments compared to bulk sediments. Deltaproteobacteria dominated the rhizosphere bacterial community where members of Geobacteraceae within the Desulfuromonadales and Desulfobacteraceae were identified. Two bacterial operational taxonomic units (OTUs) which were phylogenetically related to sulfate-reducing bacteria (SRB) became abundant in the rhizosphere. We suggest that these phylotypes could be potentially methylating bacteria and might be responsible for the higher MMHg percentage of the total Hg in rhizosphere sediments. However, SRB were not significantly favoured in rhizosphere sediments as shown by qPCR. Our findings support the hypothesis that rooted macrophytes created a microenvironment favorable for Hg methylation. The presence of E. nuttallii in Hg contaminated sediments should therefore not be overlooked.

Effect of Elodea nuttallii roots on bacterial communities and MMHg proportion in a Hg polluted sediment.

Directory of Open Access Journals (Sweden)

Nicole Regier

Full Text Available The objective of this study was to assess the effect of a rooted macrophyte Elodea nuttallii on rhizosphere bacterial communities in Hg contaminated sediments. Specimens of E. nuttallii were exposed to sediments from the Hg contaminated Babeni reservoir (Olt River, Romania in our microcosm. Plants were allowed to grow for two months until they occupied the entirety of the sediments. Total Hg and MMHg were analysed in sediments where an increased MMHg percentage of the total Hg in pore water of rhizosphere sediments was found. E. nuttallii roots also significantly changed the bacterial community structure in rhizosphere sediments compared to bulk sediments. Deltaproteobacteria dominated the rhizosphere bacterial community where members of Geobacteraceae within the Desulfuromonadales and Desulfobacteraceae were identified. Two bacterial operational taxonomic units (OTUs which were phylogenetically related to sulfate-reducing bacteria (SRB became abundant in the rhizosphere. We suggest that these phylotypes could be potentially methylating bacteria and might be responsible for the higher MMHg percentage of the total Hg in rhizosphere sediments. However, SRB were not significantly favoured in rhizosphere sediments as shown by qPCR. Our findings support the hypothesis that rooted macrophytes created a microenvironment favorable for Hg methylation. The presence of E. nuttallii in Hg contaminated sediments should therefore not be overlooked.

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

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Mohammad S. Khan

2017-07-01

Full Text Available 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.

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

Energy Technology Data Exchange (ETDEWEB)

White, Richard Allen; Rivas-Ubach, Albert; Borkum, Mark I.; Köberl, Martina; Bilbao, Aivett; Colby, Sean M.; Hoyt, David W.; Bingol, Kerem; Kim, Young-Mo; Wendler, Jason P.; Hixson, Kim K.; Jansson, Christer

2017-06-01

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 soilbased 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.

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

Science.gov (United States)

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 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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Fungal Community Successions in Rhizosphere Sediment of Seagrasses Enhalus acoroides under PAHs Stress

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Juan Ling

2015-06-01

Full Text Available Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs, but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, quantitative PCR (qPCR and a clone library have been employed to analyze the fungal community’s shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA indicated that significant factors driving community shifts were ammonium and pH (p < 0.05. Significant amounts of the variations (31.1% were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities’ changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination.

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

Science.gov (United States)

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

2015-02-01

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

Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture

Science.gov (United States)

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.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, Ruud A.; Rothballer, Michael; Strik, David P. B. T. B.; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode–rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima - ancestor of all beet crops - and modern sugar beets

Directory of Open Access Journals (Sweden)

Christin eZachow

2014-08-01

Full Text Available The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS and modern sugar beets (Beta vulgaris ssp. vulgaris cultivated in CS and potting soil (PS under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 47.4% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8% than for sugar beet (≤57.5%. Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes.

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

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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 onion promoted the growth and P uptake of tomato in phosphorus-rich soil and affected the community structure and function of phosphobacteria in tomato rhizosphere. Intercropping with potato onion also improved soil quality by lowering levels of soil acidification and salinization.

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

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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.

Arsenic in the rhizosphere soil solution of ferns.

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Wei, Chaoyang; Zheng, Huan; Yu, Jiangping

2012-12-01

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

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

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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.

Meta-scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities.

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Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Helene; Guisan, Antoine; van der Meer, Jan Roelof

2018-04-10

Interactions between plants and bacteria in the non-rhizosphere soil are rarely assessed, because they are less direct and easily masked by confounding environmental factors. By studying plant vegetation alliances and soil bacterial community co-patterning in grassland soils in 100 sites across a heterogeneous mountain landscape in the western Swiss Alps, we obtained sufficient statistical power to disentangle common co-occurrences and weaker specific interactions. Plant alliances and soil bacterial communities tended to be synchronized in community turnover across the landscape, largely driven by common underlying environmental factors, such as soil pH or elevation. Certain alliances occurring in distinct, local, environmental conditions were characterized by co-occurring specialist plant and bacterial species, such as the Nardus stricta and Thermogemmatisporaceae. In contrast, some generalist taxa, like Anthoxanthum odoratum and 19 Acidobacteria species, spanned across multiple vegetation alliances. Meta-scale analyses of soil bacterial community composition and vegetation surveys, complemented with local edaphic measurements, can thus prove useful to identify the various types of plant-bacteria interactions and the environments in which they occur.

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

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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.

No accession-specific effect of rhizosphere soil communities on the growth and competition of Arabidopsis thaliana accessions.

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Anna G Aguilera

Full Text Available Soil communities associated with specific plant species affect individual plants' growth and competitive ability. Limited evidence suggests that unique soil communities can also differentially influence growth and competition at the ecotype level. Previous work with Arabidopsis thaliana has shown that accessions produce distinct and reproducible rhizosphere bacterial communities, with significant differences in both species composition and relative abundance. We tested the hypothesis that soil communities uniquely affect the growth and reproduction of the plant accessions with which they are associated. Specifically, we examined the growth of four accessions when exposed to their own soil communities and the communities generated by each of the other three accessions. To do this we planted focal accessions inside a ring of six plants that created a "background" soil community. We grew focal plants in this design in three separate soil treatments: non-sterile soil, sterilized soil, and "preconditioned" soil. We preconditioned soil by growing accessions in non-sterile soil for six weeks before the start of the experiment. The main experiment was harvested after seven weeks of growth and we recorded height, silique number, and dry weight of each focal plant. Plants grown in the preconditioned soil treatment showed less growth relative to the non-sterile and sterile soil treatments. In addition, plants in the sterile soil grew larger than those in non-sterile soil. However, we saw no interaction between soil treatment and background accession. We conclude that the soil communities have a negative net impact on Arabidopsis thaliana growth, and that the unique soil communities associated with each accession do not differentially affect growth and competition of study species.

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

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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.

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

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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

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

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Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

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

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

2016-02-01

In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

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

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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 (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 (Psoil 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:26368339

Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

Energy Technology Data Exchange (ETDEWEB)

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

2008-10-01

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

The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and some of their structuring factors

NARCIS (Netherlands)

Buée, M.; Boer, de W.; Martin, F.; Overbeek, van L.S.; Jurkevitch, E.

2009-01-01

Rhizosphere microorganisms have two faces, like Janus the Roman god of gates and doors who symbolizes changes and transitions, from one condition to another. One face looks at the plant root, the other sees the soil. The ears and the nose sense the other gods around and the mouths are wide open,

Changes in soil bacterial communities induced by the invasive plant Pennisetum setaceum in a semiarid environment

Science.gov (United States)

Rodriguez-Caballero, Gema; Caravaca, Fuensanta; del Mar Alguacil, María; Fernández-López, Manuel; José Fernández-González, Antonio; García-Orenes, Fuensanta; Roldán, Antonio

2016-04-01

Invasive alien species are considered as a global threat being among the main causes of biodiversity loss. Plant invasions have been extensively studied from different disciplines with the purpose of identifying predictor traits of invasiveness and finding solutions. However, less is known about the implication of the rhizosphere microbiota in these processes, even when it is well known the importance of the interaction between plant rhizosphere and microbial communities. The objective of this study was to determine whether native and invasive plants support different bacterial communities in their rhizospheres and whether there are bacterial indicator species that might be contributing to the invasion process of these ecosystems. We carried out a study in five independent locations under Mediterranean semiarid conditions, where the native Hyparrhenia hirta is being displaced by Pennisetum setaceum, an aggressive invasive Poaceae and soil bacterial communities were amplified and 454-pyrosequenced. Changes in the composition and structure of the bacterial communities, owing to the invasive status of the plant, were detected when the richness and alpha-diversity estimators were calculated as well as when we analyzed the PCoA axes scores. The Indicator Species Analysis results showed a higher number of indicators for invaded communities at all studied taxonomic levels. In conclusion, the effect of the invasiveness and its interaction with the soil location has promoted shifts in the rhizosphere bacterial communities which might be facilitating the invader success in these ecosystems.

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

Science.gov (United States)

Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

2016-11-01

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

The role of rhizosphere pH in regulating the rhizosphere priming effect and implications for the availability of soil-derived nitrogen to plants.

Science.gov (United States)

Wang, Xiaojuan; Tang, Caixian

2018-01-25

A comprehensive understanding of the rhizosphere priming effect (RPE) on the decomposition of soil organic carbon (SOC) requires an integration of many factors. It is unclear how N form-induced change in soil pH affects the RPE and SOC sequestration. This study compared the change in the RPE under supply of NO3-N and NH4-N. The effect of the RPE on the mineralization of soil N and hence its availability to plant and microbes was also examined using a 15N-labelled N source. The supply of NH4-N decreased rhizosphere pH by 0.16-0.38 units, and resulted in a decreased or negative RPE. In contrast, NO3-N nutrition increased rhizosphere pH by 0.19-0.78 units, and led to a persistently positive RPE. The amounts of rhizosphere-primed C were positively correlated with rhizosphere pH. Rhizosphere pH affected the RPE mainly through influencing microbial biomass, activity and utilization of root exudates, and the availability of SOC to microbes. Furthermore, the amount of rhizosphere primed C correlated negatively with microbial biomass atom% 15N (R2 0.77-0.98, n = 12), suggesting that microbes in the rhizosphere acted as the immediate sink for N released from enhanced SOC decomposition via the RPE. N form was an important factor affecting the magnitude and direction of the RPE via its effect on rhizosphere pH. Rhizosphere pH needs to be considered in SOC and RPE modelling. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea - A Metagenomic Approach

KAUST Repository

Simoes, Marta; Antunes, Andre; Ottoni, Cristiane A.; Amini, Mohammad Shoaib; Alam, Intikhab; Alzubaidy, Hanin S.; Mokhtar, Noor Azlin; Archer, John A.C.; Bajic, Vladimir B.

2015-01-01

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 grey 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 grey 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 grey mangroves of the Red Sea, and show that they are significantly richer than previously reported.

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea - A Metagenomic Approach

KAUST Repository

Simoes, Marta

2015-11-05

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 grey 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 grey 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 grey mangroves of the Red Sea, and show that they are significantly richer than previously reported.

The mycorrhizal fungus (¤Glomus intraradices¤) affects microbial activity in the rhizosphere of pea plants (¤Pisum sativum¤)

DEFF Research Database (Denmark)

Wamberg, C.; Christensen, S.; Jakobsen, I.

2003-01-01

Pea plants were grown in gamma-irradiated soil in pots with and without addition of the AM fungus Glomus intraradices at sufficient N and limiting P. Depending on the growth phase of the plant presence of AM had negative or positive effect on rhizosphere activity. Before flowering during nutrient...... in the rhizosphere community during plant growth also supported by changes in the bacteria (DGGE). (C) 2003 Elsevier Ltd. All rights reserved....

Effects of Wheat and Faba Bean Intercropping on Microorganism Involved in Nitrogen Transformation in the Rhizosphere Soils

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TANG Yan-fen

2016-09-01

Full Text Available Soil microorganism is one of the key factors that affects soil ecological activity. It is an important symbol of soil health, and the soil nitrogen cycle is closely related to the microorganisms. The relationship between nitrogen and microorganisms under the intercropping is im-portant for the farmland ecosystem. In this paper, phospholipid fatty acids(PLFA analysis was used to determine soil microbial communi-ties, e.g., biomasses of anaerobic bacteria, aerobic bacteria, bacteria, fungi and actinobacteria. The abundance of nitrifying genes(AOB, AOA and three denitrifying genes (nirK, norB, nosZ were measured using real-time quantitative polymerase chain reaction. The enzymes, nitrate and ammonium concentrations were measured using conventional methods. The results showed that along with the growth period, the TPLFAs(total phospholipid fatty acids increased and the bacterias, fungus, actinomyces and aerobic bacterias significantly(P<0.05 dif-fered between intercropping and monoculture. The greater abundance of AOB than AOA and the variation range of 105~106 were observed in all samples. The gene copies of norB and nosZ were pronounced by intercropping in the rhizosphere of faba bean at elongation and heading stages, respectively. The abundance of nirK remarkably(P<0.05differed between intercropping and monoculture. In intercropping rhizo-sphere, the contents of NO3--N were lower than monoculture, while the NH4+-N contents were converse (P<0.05. Conclusively, wheat and fa-ba bean intercropping system could change rhizosphere microenvironment, and then the microbial community structure in the soils, which would facilitate the conservation and supplying of soil nitrogen and reduce the nitrogen loss and pollution under the intercropping conditions to some extent. This might be the nitrogen nutrition mechanism for the overyielding of wheat and faba bean intercropping system.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland.

Science.gov (United States)

He, Yuan; Hu, Wenge; Ma, Decao; Lan, Hongzhu; Yang, Yang; Gao, Yan

2017-07-01

Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 10 4 to 2.94 × 10 5 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 10 5 and 1.05 × 10 6 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH 4 + -N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina from the Red Sea — A Metagenomic Approach

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Marta Filipa Simões

2015-10-01

Full Text Available 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.

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils.

Science.gov (United States)

Alguacil, Maria Del Mar; Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-06-01

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

Science.gov (United States)

Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-01-01

ABSTRACT We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. IMPORTANCE Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels

Colonization of lettuce rhizosphere and roots by tagged Streptomyces.

Science.gov (United States)

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

2015-01-01

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

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea--A Metagenomic Approach.

Science.gov (United States)

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.

Microbial Community Dynamics and Response to Plant Growth-Promoting Microorganisms in the Rhizosphere of Four Common Food Crops Cultivated in Hydroponics.

Science.gov (United States)

Sheridan, C; Depuydt, P; De Ro, M; Petit, C; Van Gysegem, E; Delaere, P; Dixon, M; Stasiak, M; Aciksöz, S B; Frossard, E; Paradiso, R; De Pascale, S; Ventorino, V; De Meyer, T; Sas, B; Geelen, D

2017-02-01

Plant growth promoting microorganisms (PGPMs) of the plant root zone microbiome have received limited attention in hydroponic cultivation systems. In the framework of a project aimed at the development of a biological life support system for manned missions in space, we investigated the effects of PGPMs on four common food crops (durum and bread wheat, potato and soybean) cultivated in recirculating hydroponic systems for a whole life cycle. Each crop was inoculated with a commercial PGPM mixture and the composition of the microbial communities associated with their root rhizosphere, rhizoplane/endosphere and with the recirculating nutrient solution was characterised through 16S- and ITS-targeted Illumina MiSeq sequencing. PGPM addition was shown to induce changes in the composition of these communities, though these changes varied both between crops and over time. Microbial communities of PGPM-treated plants were shown to be more stable over time. Though additional development is required, this study highlights the potential benefits that PGPMs may confer to plants grown in hydroponic systems, particularly when cultivated in extreme environments such as space.

Diazotrophic Bacterial Community of Degraded Pastures

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João Tiago Correia Oliveira

2017-01-01

Full Text Available Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN of bacteria per gram of sample, in order to determine population density and calculate the Shannon-Weaver diversity index. The diversity of total diazotrophic bacterial community was determined by the technique of Denaturing Gradient Gel Electrophoresis (DGGE of the nifH gene, while the diversity of the culturable diazotrophic bacteria was determined by the Polymerase Chain Reaction (BOX-PCR technique. The increase in the degradation stage of the B. decumbens Stapf. pasture did not reduce the population density of the cultivated diazotrophic bacterial community, suggesting that the degradation at any degree of severity was highly harmful to the bacteria. The structure of the total diazotrophic bacterial community associated with B. decumbens Stapf. was altered by the pasture degradation stage, suggesting a high adaptive capacity of the bacteria to altered environments.

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

Science.gov (United States)

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

Diazotrophic Bacterial Community of Degraded Pastures

OpenAIRE

João Tiago Correia Oliveira; Everthon Fernandes Figueredo; Williane Patrícia da Silva Diniz; Lucianne Ferreira Paes de Oliveira; Pedro Avelino Maia de Andrade; Fernando Dini Andreote; Júlia Kuklinsky-Sobral; Danúbia Ramos de Lima; Fernando José Freire

2017-01-01

Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN) of bacteria per gram ...

Colonization of lettuce rhizosphere and roots by tagged Streptomyces

Directory of Open Access Journals (Sweden)

Maria eBonaldi

2015-02-01

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

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

Science.gov (United States)

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.

Probing the rhizosphere to define mineral organic relationships

Science.gov (United States)

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.

Do freshwater macrophytes influence the community structure of ammonia-oxidizing and denitrifying bacteria in the rhizospere?

DEFF Research Database (Denmark)

Herrmann, Martina; Schramm, Andreas

2006-01-01

to unvegetated sediment, especially with respect to the availability of oxygen, organic carbon, and inorganic nitrogen. We hypothesize that macrophyte species create specific niches for ammonia oxidizing and nitrate-reducing bacteria in their rhizosphere, leading to plant-dependant differences in abundance...... dortmanna have been shown to release oxygen from their roots and to stimulate nitrification and coupled nitrification-denitrification in the rhizosphere. Together with the excretion of root exudates, this effect leads to strongly modified microenvironments at the root surface and in the rhizosphere compared......-denitrification using the 15N isotope pairing technique. Ammonia-oxidizing and nitrate-reducing populations are analyzed based on the ammonia monooxygenase gene (amoA) and the nitrate reductase gene (narG) as functional markers. Preliminary data indicate that there in fact exist differences in the community composition...

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus.

Science.gov (United States)

Leff, Jonathan W; Lynch, Ryan C; Kane, Nolan C; Fierer, Noah

2017-04-01

Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere fungal communities. In particular, more modern sunflower strains had lower relative abundances of putative fungal pathogens. Seed-associated fungal communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China.

Science.gov (United States)

Bazhanov, Dmitry P; Li, Chengyun; Li, Hongmei; Li, Jishun; Zhang, Xinjian; Chen, Xiangfeng; Yang, Hetong

2016-11-08

Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation. Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA. A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins. Direct plating on SM agar enabled rapid isolation

Impact of Pore-Scale Wettability on Rhizosphere Rewetting

Directory of Open Access Journals (Sweden)

Pascal Benard

2018-04-01

Full Text Available Vast amounts of water flow through a thin layer of soil around the roots, the rhizosphere, where high microbial activity takes place—an important hydrological and biological hotspot. The rhizosphere was shown to turn water repellent upon drying, which has been interpreted as the effect of mucilage secreted by roots. The effects of such rhizosphere water dynamics on plant and microbial activity are unclear. Furthermore, our understanding of the biophysical mechanisms controlling the rhizosphere water repellency remains largely speculative. Our hypothesis is that the key to describe the emergence of water repellency lies within the microscopic distribution of wettability on the pore-scale. At a critical mucilage content, a sufficient fraction of pores is blocked and the rhizosphere turns water repellent. Here we tested whether a percolation approach is capable to predict the flow behavior near the critical mucilage content. The wettability of glass beads and sand mixed with chia seed mucilage was quantified by measuring the infiltration rate of water drops. Drop infiltration was simulated using a simple pore-network model in which mucilage was distributed heterogeneously throughout the pore space with a preference for small pores. The model approach proved capable to capture the percolation nature of the process, the sudden transition from wettable to water repellent and the high variability in infiltration rates near the percolation threshold. Our study highlights the importance of pore-scale distribution of mucilage in the emergent flow behavior across the rhizosphere.

Plant and Bird Presence Strongly Influences the Microbial Communities in Soils of Admiralty Bay, Maritime Antarctica

Science.gov (United States)

Teixeira, Lia C. R. S.; Yeargeau, Etienne; Balieiro, Fabiano C.; Piccolo, Marisa C.; Peixoto, Raquel S.; Greer, Charles W.; Rosado, Alexandre S.

2013-01-01

Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific. PMID:23840411

Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica.

Science.gov (United States)

Teixeira, Lia C R S; Yeargeau, Etienne; Balieiro, Fabiano C; Piccolo, Marisa C; Peixoto, Raquel S; Greer, Charles W; Rosado, Alexandre S

2013-01-01

Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.

Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica.

Directory of Open Access Journals (Sweden)

Lia C R S Teixeira

Full Text Available Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies, Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization

DEFF Research Database (Denmark)

Wolters, Birgit; Jacquiod, Samuel Jehan Auguste; Sørensen, Søren Johannes

2018-01-01

Organic soil fertilizers, such as livestock manure and biogas digestate, frequently contain bacteria carrying resistance genes (RGs) to antimicrobial substances and mobile genetic elements (MGEs). The effects of different fertilizers (inorganic, manure, digestate) on RG and MGE abundance...... and microbial community composition were investigated in a field plot experiment. The relative abundances of RGs [sul1, sul2, tet(A), tet(M), tet(Q), tet(W), qacEΔ1/qacE] and MGEs [intI1, intI2, IncP-1, IncP-1ε and LowGC plasmids] in total community (TC)-DNA from organic fertilizers, bulk soil and maize......, integrons and few genera affiliated to Bacteroidetes and Firmicutes in bulk soil, while digestate increased sul2, tet(W) and intI2. At harvest, treatment effects vanished in bulk soil. However, organic fertilizer effects were still detectable in the rhizosphere for RGs [manure: intI1, sul1; digestate: tet...

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

Science.gov (United States)

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.

Dissipation of 14C chlorpyrifos in the rhizosphere of rice

International Nuclear Information System (INIS)

Sharungbam, Geeta Devi; Kapadnis, B.P.; Deopurkar, R.L.; Kale, S.P.

2004-01-01

The root exudates from the plants contribute to the biodegradation of insecticides. Although, different mechanisms have been proposed, there is no clear elucidation of any mechanism. This study investigates the dissipation of an organophosphorus insecticide, chlorpyrifos in the rhizospheric soil planted with rice plant. Two sets of experimental tanks were maintained with or without plants using soil spiked with 1 mg kg -1 and 10 mg kg -1 of chlorpyrifos. Experiment was conducted for 180 days till the rice plant starts bearing seeds. The 14 C activity decreased rapidly in the rhizospheric soil as compare to the non-rhizospheric soil. The total culturable microflora were higher in the rhizospheric than the non-rhizospheric soil. The plant extract had given few counts indicating some negligible amount of chlorpyrifos uptake. The 14 C activity in the water was disappeared after 30 days. It was observed that very low amount of residue persisted in soil. This studies revealed that the plants play an important role in the dissipation of the chlorpyrifos from the rice flooded rhizospheric soil. (author)

Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.

Directory of Open Access Journals (Sweden)

Özgül Inceoğlu

Full Text Available BACKGROUND: Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process. METHODOLOGY/PRINCIPAL FINDINGS: DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample. Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria. Principal components analyses revealed that rhizosphere samples were significantly different from corresponding bulk soil in each growth stage. Furthermore, cultivar effects were found in the young plant stage, whereas these became insignificant in the flowering and senescence stages. Besides, an effect of time of season was observed for both rhizosphere and bulk soils. The analyzed rhizosphere samples of the potato cultivars were grouped into two groups, in accordance with the allocation of carbon to starch in their tubers, i.e. Aveka, Aventra and Karnico (high versus Premiere and Desiree (low and thus replicates per group were established. CONCLUSIONS: Across all potato cultivars, the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages. Furthermore, Pseudomonas, Beta-, Alpha- and

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation.

Science.gov (United States)

Koebernick, Nicolai; Daly, Keith R; Keyes, Samuel D; George, Timothy S; Brown, Lawrie K; Raffan, Annette; Cooper, Laura J; Naveed, Muhammad; Bengough, Anthony G; Sinclair, Ian; Hallett, Paul D; Roose, Tiina

2017-10-01

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm -3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

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

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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

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

Science.gov (United States)

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

2016-02-01

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

Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia

KAUST Repository

Osman, Jorge R.; Zelicourt, Axel de; Bisseling, Ton; Geurts, Rene; Hirt, Heribert; DuBow, Michael S.

2016-01-01

Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities

Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia

KAUST Repository

Osman, Jorge R.

2016-04-08

Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities

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

Science.gov (United States)

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

[Effects of transgenic Bt + CpTI cotton on rhizosphere bacteria and ammonia oxidizing bacteria population].

Science.gov (United States)

Dong, Lianhua; Meng, Ying; Wang, Jing

2014-03-04

The effect of transgenic cotton on the rhizosphere bacteria can be important to the risk assessment for the genetically modified crops. We studied the rhizosphere microbial community with cultivating genetically modified cotton. The effects of transgenic Bt + CpTI Cotton (SGK321) and its receptor cotton (SY321) on rhizosphere total bacteria and ammonia oxidizing bacteria population size were studied by using droplet digital PCR. We collected rhizosphere soil before cotton planting and along with the cotton growth stage (squaring stage, flowering stage, belling stage and boll opening stage). There was no significant change on the total bacterial population between the transgenic cotton and the receptor cotton along with the growth stage. However, the abundance of ammonia oxidizing bacteria (AOB) in both type of cottons showed significant difference between different growth stages, and the variation tendency was different. In squaring stage, the numbers of AOB in rhizosphere of SY321 and SGK321 increased 4 and 2 times, respectively. In flowering stage, AOB number in rhizosphere of SY321 significantly decreased to be 5.96 x 10(5) copies/g dry soil, however, that of SGK321 increased to be 1.25 x 10(6) copies/g dry soil. In belling stage, AOB number of SY321 greatly increased to be 1.49 x 10(6) copies/g dry soil, but no significant change was observed for AOB number of SGK321. In boll opening stage, both AOB number of SY321 and SGK321 clearly decreased and they were significantly different from each other. Compared to the non-genetically modified cotton, the change in abundance of ammonia oxidizing bacteria was slightly smooth in the transgenic cotton. Not only the cotton growth stage but also the cotton type caused this difference. The transgenic cotton can slow down the speed of ammonia transformation through impacting the number of AOB, which is advantageous for plant growth.

Potato cultivar type affects the structure of ammonia oxidizer communities in field soil under potato beyond the rhizosphere

NARCIS (Netherlands)

Cavalcante Franco Dias, A.; Hoogwout, E.F.; de Cassia Pereira e Silva, M.; Falcão Salles, J.; van Overbeek, L.S.; van Elsas, J.D.

The effects of plants on the microbiota involved in the oxidation of ammonia in soils have been controversial. Here, we investigated the dynamics in the abundances and community structures of the bacterial and archaeal ammonia oxidizers (AOB and AOA, respectively) in two fields that were cropped

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

Science.gov (United States)

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

Relevance of extracellular DNA in rhizosphere

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Experimental warming effects on the bacterial community structure and diversity

Science.gov (United States)

Kim, W.; Han, S.; Adams, J.; Son, Y.

2014-12-01

The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

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

Science.gov (United States)

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.

The mechanism on rhizosphere phosphorus activation of two wheat ...

African Journals Online (AJOL)

The mechanism on rhizosphere phosphorus activation of two wheat genotypes with different phosphorus efficiency. ... genotype would be a potential approach for maintaining wheat yield potential in soils with low P bioavailability. Key words: Wheat, P efficiency, rhizosphere properties, P fractions, phosphates activity.

In vitro screening of selected herbicides on rhizosphere mycoflora ...

African Journals Online (AJOL)

In vitro screening of five selected herbicides at different concentrations on rhizosphere mycoflora from yellow pepper (capsicum annum L var. Nsukka yellow) seedlings at Nsukka were investigated. The herbicides employed for this study were Paraquat, Glyphosate, Primextra, Atrazine and Linuron. The isolated rhizosphere ...

[Influence of Mirabilis jalapa Linn. Growth on the Microbial Community and Petroleum Hydrocarbon Degradation in Petroleum Contaminated Saline-alkali Soil].

Science.gov (United States)

Jiao, Hai-hua; Cui, Bing-jian; Wu, Shang-hua; Bai, Zhi-hui; Huang, Zhan-bin

2015-09-01

In order to explore the effect of Mirabilis jalapa Linn. growth on the structure characteristics of the microbial community and the degradation of petroleum hydrocarbon (TPH) in the petroleum-contaminated saline-alkali soil, Microbial biomass and species in the rhizosphere soils of Mirabilis jalapa Linn. in the contaminated saline soil were studied with the technology of phospholipid fatty acids (PLFAs) analysis. The results showed that comparing to CK soils without Mirabilis jalapa Linn., the ratio of PLFAs species varied were 71. 4%, 69. 2% and 33. 3% in the spring, summer and autumn season, respectively. In addition, there was distinct difference of the biomasses of the microbial community between the CK and rhizosphere soils and among the difference seasons of growth of Mirabilis jalapa Linn.. Compare to CK soil, the degradation rates of total petroleum hydrocarbon (TPH) was increased by 47. 6%, 28. 3%, and 18. 9% in spring, summer, and autumn rhizosphere soils, respectively. Correlation analysis was used to determine the correlation between TPH degradation and the soil microbial community. 77. 8% of the total soil microbial PLFAs species showed positive correlation to the TPH degradation (the correlation coefficient r > 0), among which, 55. 6% of PLFAs species showed high positive correlation(the correlation coefficient was r≥0. 8). In addition, the relative content of SAT and MONO had high correlation with TPH degradation in the CK sample soils, the corelation coefficient were 0. 92 and 0. 60 respectively; However, the percent of positive correlation was 42. 1% in the rhizosphere soils with 21. 1% of them had high positive correlation. The relative content of TBSAT, MONO and CYCLO had moderate or low correlation in rhizosphere soils, and the correlation coefficient were 0. 56, 0. 50, and 0. 07 respectively. Our study showed that the growth of mirabilis Mirabilis jalapa Linn. had a higher influence on the species and biomass of microbial community in the

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

Science.gov (United States)

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.

Jerusalem artichoke decreased salt content and increased diversity of bacterial communities in the rhizosphere soil in the coastal saline zone

Science.gov (United States)

Shao, Tianyun; Li, Niu; Cheng, Yongwen; Long, Xiaohua; Shao, Hongbo; Zed, Rengel

2017-04-01

Soil salinity is one of the main environmental constraints that restrict plant growth and agricultural productivity; however, utilization of salt-affected land can bring substantial benefits. This study used an in-situ remediation method by planting Jerusalem artichoke in naturally occurring saline alkali soils with different salinity (high salinity (H, >4.0 g•salt kg-1 soil), moderate salinity (M, 2.0-4.0 g•salt kg-1 soil) and low salinity (L, 1.0-2.0 g•salt kg-1 soil) in the coastal saline zone in southeast China in comparison with the respective controls without Jerusalem artichoke planting (undisturbed soil). Soil pH and salinity increased sequentially from the rhizosphere to the bulk soil and the unplanted controls. The activity of neutral phosphatase and invertase decreased in the order L > M > H, whereas that of catalase was reverse. The minimum content of calcite, muscovite and quartz, and maximum content of chlorite and albite, were found in the control soils. Planting of Jerusalem artichoke enhanced bacterial microflora in saline alkali soil. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. The number of Operational Taxonomic Units (OTU) in the rhizosphere soil was, respectively, 1.27, 1.02 and 1.25 times higher compared with the bulk soil, suggesting that Jerusalem artichoke played a significant role in increasing abundance and diversity of soil microbial populations. The study showed that Jerusalem artichoke could be used to improve saline alkali soil by enriching bacterial communities, enhancing the activity of phosphatase and invertase, and decreasing soil salinity.

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

International Nuclear Information System (INIS)

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. - Highlights: • Most flame retardants were enriched in rhizosphere soils compared to bulk soils. • Rhizosphere effects were more significant for NBFRs than for PBDEs. • PBDEs were significantly correlated with the total organic carbon in soils. • Result suggested that PBDEs have not been replaced by other BFRs in the e-waste. - The influences of rhizosphere effects on the distributions of PBDEs, NBFRs, and DPs in soils were different.

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

Directory of Open Access Journals (Sweden)

Sandra Granzow

2017-05-01

Full Text Available Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating

Carbon transfer in soil - plant system. Molecular labelling utilization for determining rhizosphere compounds

International Nuclear Information System (INIS)

Leguay, J.J.

2000-01-01

The growing up of the bacteria developing in the rhizosphere of plants is dependent on the compounds exudation by plant roots. Even the bacterial genetics use has permitted to identify diverse functions involved in the process of the rhizosphere colonisation ( mobility, heterotrophic bacteria, growing rate, antibiotics production), there is a big delay in vegetal partners. To decrease this delay we tried to characterize the interactions between a plant model, Arabidopsis thaliana and the rhizosphere bacteria. An experimental device has been conceived for measuring the transfer of carbon issued from the photosynthesis to roots and soil. The exudation by roots has been studied. The analysis of rhizospheric compounds in situ pose some methodological problems, especially, the rhizospheric compounds must be extracted from the soil matrix. we suggest an analysis method of rhizospheric compound and of their dynamics. (F.M.)

Submerged macrophytes modify bacterial community composition in sediments in a large, shallow, freshwater lake.

Science.gov (United States)

Zhao, Da-Yong; Liu, Peng; Fang, Chao; Sun, Yi-Meng; Zeng, Jin; Wang, Jian-Qun; Ma, Ting; Xiao, Yi-Hong; Wu, Qinglong L

2013-04-01

Submerged aquatic macrophytes are an important part of the lacustrine ecosystem. In this study, the bacterial community compositions in the rhizosphere sediments from three kinds of submerged macrophytes (Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans) were investigated to determine whether submerged macrophytes could drive the variation of bacterial community in the eutrophic Taihu Lake, China. Molecular techniques, including terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries, were employed to analyze the bacterial community compositions. Remarkable differences of the T-RFLP patterns were observed among the different samples, and the results of LIBSHUFF analysis also confirmed that the bacterial community compositions in the rhizosphere sediments of three kinds of submerged macrophytes were statistically different from that of the unvegetated sediment. Acidobacteria, Deltaproteobacteria, and Betaproteobacteria were the dominant bacterial groups in the rhizosphere sediments of Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans, respectively, accounting for 15.38%, 29.03%, and 18.00% of the total bacterial abundances. Our study demonstrated that submerged macrophytes could influence the bacterial community compositions in their rhizosphere sediments, suggesting that macrophytes have an effect on the cycling and transportation of nutrients in the freshwater lake ecosystem.

Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

Science.gov (United States)

Hubert, Nathaniel A; Gehring, Catherine A

2008-09-01

Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

Elucidating rhizosphere processes by mass spectrometry - A review.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

The mechanism on rhizosphere phosphorus activation of two wheat ...

African Journals Online (AJOL)

Yomi

2012-01-24

Jan 24, 2012 ... This fact particularly applies to soils with a high iron or aluminum oxide ... phorus stress conditions, the P efficient genotype can take advantage .... In this method, 1-mm thick stainless steel pane was .... amount of root-derived C flow through the rhizosphere ...... rhizosphere carbon flow modelling. Plant Soil.

Dechlorination of PCBs in the rhizosphere of switchgrass and poplar

International Nuclear Information System (INIS)

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

2013-01-01

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. -- Highlights: •Soil was spiked and aged and then planted with poplar and switchgrass. •Planted microcosms showed significant reductive dechlorination and greater biotransformation than unplanted reactor. •Rhizospheric reductive dechlorination pathways are proposed. -- This study provides insight into rhizospheric transformation of PCBs

Bacterial incorporation of tritiated thymidine and populations of bacteriophagous fauna in the rhizosphere of wheat

DEFF Research Database (Denmark)

Christensen, Henrik; Griffiths, Bryan; Christensen, Søren

1992-01-01

Bacterial and microfaunal populations, and bacterial productivity measured by tritiated thymidine (3HTdr) incorporation, in the rhizosphere of wheat seedlings were measured. Soil from planted pots was fractionated into rhizosphere and non-rhizosphere (bulk) soil, while unplanted soil was taken from...... pots without plants. Total bacterial counts and biovolume did not differ between fractions but viable (plate) counts were 8 times higher in the rhizosphere compared to bulk and unplanted soil. 3HTdr was incorporated at a constant rate with low variability in bulk or unplanted soil. In rhizosphere soil...... 3HTdr incorporation was lower than in bulk or unplanted soils and showed high variability. The populations of bacterial-feeding protozoa and nematodes indicated that rhizosphere bacterial activity was actually 3–4 times greater in rhizosphere than bulk soil in accordance with the results...

Elucidating rhizosphere processes by mass spectrometry – A review

International Nuclear Information System (INIS)

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

2017-01-01

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. - Highlights: • State-of-the-art mass spectrometry methods developed and applied in rhizosphere research are reviewed. • Elemental and molecular mass spectrometry emphasizing different separation techniques (GC, LC or CE) are discussed. • Case studies on metal detoxification and

Elucidating rhizosphere processes by mass spectrometry – A review

Energy Technology Data Exchange (ETDEWEB)

Rugova, Ariana [Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences-BOKU, Vienna (Austria); Puschenreiter, Markus [Department of Forest and Soil Sciences, Rhizosphere Ecology and Biogeochemistry Group, University of Natural Resources and Life Sciences-BOKU, Vienna (Austria); Koellensperger, Gunda [Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna (Austria); Hann, Stephan, E-mail: stephan.hann@boku.ac.at [Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences-BOKU, Vienna (Austria)

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. - Highlights: • State-of-the-art mass spectrometry methods developed and applied in rhizosphere research are reviewed. • Elemental and molecular mass spectrometry emphasizing different separation techniques (GC, LC or CE) are discussed. • Case studies on metal detoxification

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

Science.gov (United States)

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

Metagenomic assesment of the potential microbial nitrogen pathways in the rhizosphere of a Mediterranean forest after wildfire

OpenAIRE

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

2015-01-01

Wildfires are frecuent in the forest 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 nitrgen cycle,. We explored the effetcs 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 u...

Rhizosphere Biological Processes of Legume//Cereal Intercropping Systems: A Review

Directory of Open Access Journals (Sweden)

JIANG Yuan-yuan

2016-09-01

Full Text Available Intercropping, a sustainable planting pattern, was widely used in the wordwide. It not only has the advantages of yield and nutrient acquisition, but also can ensure food security and reduce the risk of crop failures. The majority of intercropping systems involve legume//cereal combinations because of interspecific facilitation or complementarity. The rhizosphere is the interface between plants and soil where there are interactions among a myriad of microorganisms and affect the uptake of nutrients, water and harmful substances. The rhizosphere biologi-cal processes not only determine the amount of nutrients and the availability of nutrients, but also affect crop productivity and nutrient use efficiency. Hence, this paper summarized the progress made on root morphology, rhizosphere microorganisms, root exudates and ecological ef-fect in the perspective of the rhizosphere biological process,which would provide theoretical basis for improving nutrient availability, remov-ing heavy metals, and plant genetic improvements.

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression

NARCIS (Netherlands)

van der Voort, M.; Kempenaar, M.; van Driel, M.; Raaijmakers, J.M.; Mendes, R.

2016-01-01

The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic

Selective progressive response of soil microbial community to wild oat roots

Energy Technology Data Exchange (ETDEWEB)

DeAngelis, K.M.; Brodie, E.L.; DeSantis, T.Z.; Andersen, G.L.; Lindow, S.E.; Firestone, M.K.

2008-10-01

Roots moving through soil enact physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. Use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies previously reported compositional changes, including increases in chitinase and protease specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change in 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA T-RFLP analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared to bulk soil, but then increased in older root zones. Quantitative PCR revealed {beta}-Proteobacteria and Actinobacteria present at about 10{sup 8} copies of 16S rRNA genes g{sup -1} soil, with Nitrospira having about 10{sup 5} copies g{sup -1} soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in function in progressively more mature rhizosphere zones.

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression

NARCIS (Netherlands)

Voort, van der M.; Kempenaar, Marcel; Driel, van Marc; Raaijmakers, Jos M.; Mendes, Rodrigo

2016-01-01

The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic

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

Directory of Open Access Journals (Sweden)

François eThomas

2014-06-01

Full Text Available 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.

Rhizosphere characteristics of indigenously growing nickel hyperaccumulator and excluder plants on serpentine soil

International Nuclear Information System (INIS)

Wenzel, W.W.; Bunkowski, M.; Puschenreiter, M.; Horak, O.

2003-01-01

Field study reinforces that root exudates may contribute to nickel hyperaccumulation in Thlaspi goesingense Halacsy. - The role of rhizosphere processes in metal hyperaccumulation is largely unexplored and a matter of debate, related field data are virtually not available. We conducted a field survey of rhizosphere characteristics beneath the Ni hyperaccumulator Thlaspi goesingense Halacsy and the metal-excluder species Silene vulgaris L. and Rumex acetosella L. growing natively on the same serpentine site. Relative to bulk soil and to the rhizosphere of the excluder species, we found significantly increased DOC and Ni concentrations in water extracts of T. goesingense rhizosphere, whereas exchangeable Ni was depleted due to excessive uptake of Ni. Chemical speciation analysis using the MINTEQA2 software package revealed that enhanced Ni solubility in Thlaspi rhizosphere is driven by the formation of Ni-organic complexes. Moreover, ligand-induced dissolution of Ni-bearing minerals is likely to contribute to enhanced Ni solubility. Increased Mg and Ca concentrations and pH in Thlaspi rhizosphere are consistent with ligand-induced dissolution of orthosilicates such as forsterite (Mg 2 SiO 4 ). Our field data reinforce the hypothesis that exudation of organic ligands may contribute to enhanced solubility and replenishment of metals in the rhizosphere of hyperaccumulating species

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

Science.gov (United States)

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

NARCIS (Netherlands)

Rasche, F; Hodl, [No Value; Poll, C; Kandeler, E; Gerzabek, MH; van Elsas, JD; Sessitsch, A

A greenhouse experiment was performed to analyze a potential effect of genetically modified potatoes expressing antibacterial compounds (attacin/cecropin, T4 lysozyme) and their nearly isogenic, nontransformed parental wild types on rhizosphere bacterial communities. To compare plant

Feasibility study on the application of rhizosphere microflora of rice for the biohydrogen production from wasted bread

Energy Technology Data Exchange (ETDEWEB)

Doi, Tetsuya [Field Production Science Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002 (Japan); Nishihara Environment Technology Inc., Tokyo 108-0023 (Japan); Matsumoto, Hisami [Nishihara Environment Technology Inc., Tokyo 108-0023 (Japan); Abe, Jun [AE-Bio, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657 (Japan); Morita, Shigenori [Field Production Science Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002 (Japan)

2009-02-15

We performed an experiment of continuous anaerobic hydrogen fermentation as a pilot-plant-scale test, in which waste from a bread factory was fermented by microflora of rice rhizosphere origin. The community structure of microflora during anaerobic hydrogen fermentation was analyzed using PCR-DGGE, FISH, and quinone profiles. The relation of those results to hydrogen generation was discussed. Results show that a suitable condition was a reactor temperature of 35 C, with HRT 12-36 h, volume load of 30-70 kg-COD{sub Cr}/m{sup 3} day, and maximum hydrogen production rate of 1.30 mol-H{sub 2}/mol-hexose. Regarding characteristics of microflora during fermentation, PCR-DGGE results show specific 16S rDNA band patterns; Megasphaera elsdenii and Clostridium sp. of the hydrogen-producing bacteria were identified. M. elsdenii was detected throughout the fermentation period, while Clostridium sp. of hydrogen-producing bacteria was detected on the 46th day. Furthermore, FISH revealed large amounts of Clostridium spp. in the sample. The quinone profile showed that the dominant molecular species of quinone is MK-7. Because Clostridium spp. belong to MK-7, results suggest that the quinone profile result agrees with the results of PCR-DGGE and FISH. Microflora in the rhizosphere of rice plants can be a possible resource for effective bacteria of biohydrogen production. (author)

Effect of Genetically Modified Poplars on Soil Microbial Communities during the Phytoremediation of Waste Mine Tailings▿†

Science.gov (United States)

Hur, Moonsuk; Kim, Yongho; Song, Hae-Ryong; Kim, Jong Min; Choi, Young Im; Yi, Hana

2011-01-01

The application of transgenic plants to clean up environmental pollution caused by the wastes of heavy metal mining is a promising method for removing metal pollutants from soils. However, the effect of using genetically modified organisms for phytoremediation is a poorly researched topic in terms of microbial community structures, despite the important role of microorganisms in the health of soil. In this study, a comparative analysis of the bacterial and archaeal communities found in the rhizosphere of genetically modified (GM) versus wild-type (WT) poplar was conducted on trees at different growth stages (i.e., the rhizospheres of 1.5-, 2.5-, and 3-year-old poplars) that were cultivated on contaminated soils together with nonplanted control soil. Based on the results of DNA pyrosequencing, poplar type and growth stages were associated with directional changes in the structure of the microbial community. The rate of change was faster in GM poplars than in WT poplars, but the microbial communities were identical in the 3-year-old poplars. This phenomenon may arise because of a higher rate and greater extent of metal accumulation in GM poplars than in naturally occurring plants, which resulted in greater changes in soil environments and hence the microbial habitat. PMID:21890678

Colonization of lettuce rhizosphere and roots by tagged Streptomyces

OpenAIRE

Maria eBonaldi; Xiaoyulong eChen; Andrea eKunova; Cristina ePizzatti; Marco eSaracchi; Paolo eCortesi

2015-01-01

Beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. We studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified Streptomyces spp. Five Streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, Sclerotinia sclerotiorum, were transformed with pIJ8641 plas...

Leveraging disjoint communities for detecting overlapping community structure

International Nuclear Information System (INIS)

Chakraborty, Tanmoy

2015-01-01

Network communities represent mesoscopic structure for understanding the organization of real-world networks, where nodes often belong to multiple communities and form overlapping community structure in the network. Due to non-triviality in finding the exact boundary of such overlapping communities, this problem has become challenging, and therefore huge effort has been devoted to detect overlapping communities from the network.In this paper, we present PVOC (Permanence based Vertex-replication algorithm for Overlapping Community detection), a two-stage framework to detect overlapping community structure. We build on a novel observation that non-overlapping community structure detected by a standard disjoint community detection algorithm from a network has high resemblance with its actual overlapping community structure, except the overlapping part. Based on this observation, we posit that there is perhaps no need of building yet another overlapping community finding algorithm; but one can efficiently manipulate the output of any existing disjoint community finding algorithm to obtain the required overlapping structure. We propose a new post-processing technique that by combining with any existing disjoint community detection algorithm, can suitably process each vertex using a new vertex-based metric, called permanence, and thereby finds out overlapping candidates with their community memberships. Experimental results on both synthetic and large real-world networks show that PVOC significantly outperforms six state-of-the-art overlapping community detection algorithms in terms of high similarity of the output with the ground-truth structure. Thus our framework not only finds meaningful overlapping communities from the network, but also allows us to put an end to the constant effort of building yet another overlapping community detection algorithm. (paper)

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

NARCIS (Netherlands)

Philippot, L.; Raaijmakers, J.M.; Lemanceau, P.; Van der Putten, W.H.

2013-01-01

The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its

Changes of organic acid exudation and rhizosphere pH in rice plants under chromium stress

International Nuclear Information System (INIS)

Zeng Fanrong; Chen Song; Miao Ying; Wu Feibo; Zhang Guoping

2008-01-01

The effect of chromium (Cr) stress on the changes of rhizosphere pH, organic acid exudation, and Cr accumulation in plants was studied using two rice genotypes differing in grain Cr accumulation. The results showed that rhizosphere pH increased with increasing level of Cr in the culture solution and with an extended time of Cr exposure. Among the six organic acids examined in this experiment, oxalic and malic acid contents were relatively higher, and had a significant positive correlation with the rhizosphere pH, indicating that they play an important role in changing rhizosphere pH. The Cr content in roots was significantly higher than that in stems and leaves. Cr accumulation in plants was significantly and positively correlated with rhizosphere pH, and the exudation of oxalic, malic and citric acids, suggesting that an increase in rhizosphere pH, and exudation of oxalic, malic and citric acid enhances Cr accumulation in rice plants. - Rhizosphere pH and organic acid exudation of rice roots are markedly affected by chromium level in culture solution

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

Directory of Open Access Journals (Sweden)

Ahmed Elhady

2018-06-01

Full Text Available 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

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

Science.gov (United States)

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

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

Science.gov (United States)

Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2014-05-01

detritivore communities in the soil. The kinetics (Km and Vmax) of four extracellular hydrolytic enzymes responsible for C- and phosphorous-cycle (β-glucosidase, β-xylosidase, β-cellobiohydrolase and acid phosphatase), microbial biomass, basal respiration (BR) and substrate-induced respiration (SIR) were measured in rhizosphere, detritusphere and control from 0 - 10 and 10 - 20 cm. The metabolic quotient (qCO2) was calculated as specific indicator for efficiency of microbial substrate utilization. We observed clear differences in enzymes activities at low and high concentrations of substrate. At substrate saturation enzyme activity rates of were significantly higher in rooted plots compared to litter amended plots, whereas at lower concentration no treatment effect could be found. The BR, SIR and qCO2 values were significantly higher at 0 - 10 cm of the planted treatment compared to litter and control plots, revealing a significantly higher respiration at lower efficiency of microbial substrate utilization in the rhizosphere. The Michaelis-Menten constant (Km) decreased with depth, especially for β-glucosidase, acid phosphatase and β-xylosidase, indicating higher substrate affinity of microorganisms in deeper soil and therefore different enzyme systems functioning. The substrate affinity factor (Vmax/Km) increased 2-fold with depth for various enzymes, reflecting a switch of predominantly occurring microbial strategies. Vmax/Km ratio indicated relative domination of zymogenous microbial communities (r-strategists) in 0 - 10 cm depth as compared with 10 - 20 cm depth where the K-strategists dominated.

Metabolic and phylogenetic analysis of microbial communities during phytoremediation of soil contaminated with weathered hydrocarbons and heavy metals.

Science.gov (United States)

Palmroth, Marja R T; Koskinen, Perttu E P; Kaksonen, Anna H; Münster, Uwe; Pichtel, John; Puhakka, Jaakko A

2007-12-01

In the current study, the microbial ecology of weathered hydrocarbon and heavy metal contaminated soil undergoing phytoremediation was studied. The relationship of functional diversity, measured as carbon source utilisation in Biolog plates and extracellular enzymatic activities, and genetic diversity of bacteria was evaluated. Denaturing gradient gel electrophoresis was used for community analyses at the species level. Bulk soil and rhizosphere soil from pine and poplar plantations were analysed separately to determine if the plant rhizosphere impacted hydrocarbon degradation. Prevailing microbial communities in the field site were both genetically and metabolically diverse. Furthermore, both tree rhizosphere and fertilisation affected the compositions of these communities and increased activities of extracellular aminopeptidases. In addition, the abundance of alkane hydroxylase and naphthalene dioxygenase genes in the communities was low, but the prevalence of these genes was increased by the addition of bioavailable hydrocarbons. Tree rhizosphere communities had greater hydrocarbon degradation potential than those of bulk soil. Hydrocarbon utilising communities were dominated generally by the species Ralstonia eutropha and bacteria belonging to the genus Burkholderia. Despite the presence of viable hydrocarbon-degrading microbiota, decomposition of hydrocarbons from weathered hydrocarbon contaminated soil over four years, regardless of the presence of vegetation, was low in unfertilised soil. Compost addition enhanced the removal of hydrocarbons.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

Science.gov (United States)

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora

DEFF Research Database (Denmark)

Herrmann, Martina; Saunders, Aaron M.; Schramm, Andreas

2008-01-01

Archaeal and bacterial ammonia monooxygenase genes (amoA) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrifi...

Soil nematode community under the non-native trees in the Botanic Garden of Petrozavodsk State University

Directory of Open Access Journals (Sweden)

Sushchuk Anna

2016-12-01

Full Text Available The particularities of soil nematode communities of the rhizosphere of non-native trees were studied in the Botanic Garden of Petrozavodsk State University (Republic of Karelia. Taxonomic diversity, abundance, community structure and ecological indices derived from nematode fauna analysis were used as the evaluation parameters. Nematode fauna included 51 genera, 6 of them were plant parasitic. The dominant eco-trophic group in the nematode community structure of coniferous trees was bacterial feeders; fungal feeders in most cases were observed in the second numbers. The contribution of bacterial feeders was decreased and plant parasites were increased in eco-trophic structure of nematode communities of deciduous trees in compared with coniferous trees. Analysis of ecological indices showed that the state of soil nematode communities reflects complex, structured (stable soil food web in the biocenoses with deciduous trees, and degraded (basal food web – under coniferous trees.

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

Science.gov (United States)

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.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell.

Science.gov (United States)

Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-04-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

Energy Technology Data Exchange (ETDEWEB)

Timmers, Ruud A.; Strik, David P.B.T.B.; Hamelers, Bert; Buisman, Cees [Wageningen Univ. (Netherlands). Sub-dept. of Environmental Technology; Rothballer, Michael; Hartmann, Anton [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Microbe-Plant Interactions; Engel, Marion; Schulz, Stephan; Schloter, Michael [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Terrestrial Ecogenetics

2012-04-15

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors. (orig.)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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 heavy metal phytoextraction.

Effects of Continuous Cropping on Bacterial Flora Structure in Soybean Rhizosphere Soil%连作对大豆根际土壤细菌菌群结构的影响

Institute of Scientific and Technical Information of China (English)

殷继忠; 李亮; 接伟光; 蔡柏岩

2018-01-01

土壤细菌的菌群结构是土壤生态环境质量的重要组成部分.为探明大豆连作种植后根际土壤细菌群落结构变化,试验选取连作0年大豆根际土样与连作2年大豆根际土壤,利用Illumina高通量测序技术对比研究了其中的细菌群落结构.结果表明,连作0年根际土壤中的细菌丰富度和多样性指数均高于连作2年大豆根际土壤中相应值.大豆根际土壤中的噬纤维菌科(Cytophagaceae)、鞘氨纯单胞菌(Sphingomonas)、慢生根瘤菌(Bradyrhizobium)及链霉菌属(Streptomyces)等一些有益菌的相对丰度要变化并不显著.大豆连作会降低土壤的细菌多样性,改变细菌菌群结构.但是在短期连作过程中,不同作物根际微生物类群的变化规律各不相同,难以用来推断作物连作所存在普遍现象.以期试验结果同时为缓解短期大豆连作障碍提高大豆产量提供一定的理论依据.%The flora structure of soil bacteria is an important part of soil ecological environment quality. In order to find out the changes of bacterial flora structure in the rhizosphere soil after continuous cropping of soybean,soybean rhizosphere soil samples of zero- and 2-year of continuous cropping were selected,and their bacterial flora structures were studied using Illumina high-throughput sequencing technique. The results showed that the bacterial abundances and diversity indexes in the rhizosphere soil of zero-year continuous cropping were higher than those of the rhizosphere soil of 2-year continuous cropping. The abundances of these beneficial bacteria Cytophagaceae,Sphingomonas, Bradyrhizobium,and Streptomyces varied insignificantly. Soybean continuous cropping reduced the bacterial diversity of the soil and changed the bacterial flora structure. However,during the short-term continuous cropping process,the variation pattern of rhizosphere microbes in different crops differed,thus it was difficult to infer a common phenomenon resulted

Investigations into rhizosphere microflora. IV. Fungal association in different root regions of some rainy-season crops

Directory of Open Access Journals (Sweden)

V. B. Srivastava

2015-01-01

Full Text Available Non-rhizosphere, rhizosphere and rhizoplane microflora of the crown and distal regions of Echinochloa crusgalli (L. Beauv. and Paspalum scrobiculatum L. were studied from seedling stage to the harvest. The variation in bacterial and fungal flora in relation to host species, stage of development and żonę of the rhizosphere were studied. The differences between fungal and bacterial flora are described. The relation between rhizosphere microflora and roots exudates is described.

Significance of treated agrowaste residue and autochthonous inoculates (Arbuscular mycorrhizal fungi and Bacillus cereus) on bacterial community structure and phytoextraction to remediate soils contaminated with heavy metals.

Science.gov (United States)

Azcón, Rosario; Medina, Almudena; Roldán, Antonio; Biró, Borbála; Vivas, Astrid

2009-04-01

In this study, we analyzed the impact of treatments such as Aspergillus niger-treated sugar beet waste (SB), PO4(3-) fertilization and autochthonous inoculants [arbuscular mycorrhizal (AM) fungi and Bacillus cereus], on the bacterial community structure in a soils contaminated with heavy metals as well as, the effectiveness on plant growth (Trifolium repens). The inoculation with AM fungi in SB amended soil, increased plant growth similarly to PO4(3-) addition, and both treatments matched in P acquisition but bacterial biodiversity estimated by denaturing gradient gel electrophoresis of amplified 16S rDNA sequences, was more stimulated by the presence of the AM fungus than by PO4(3-) fertilization. The SB amendment plus AM inoculation increased the microbial diversity by 233% and also changed (by 215%) the structure of the bacterial community. The microbial inoculants and amendment used favoured plant growth and the phytoextraction process and concomitantly modified bacterial community in the rhizosphere; thus they can be used for remediation. Therefore, the understanding of such microbial ecological aspects is important for phytoremediation and the recovery of contaminated soils.

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

Science.gov (United States)

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.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica

OpenAIRE

Mesa, Victoria; Navazas, Alejandro; Gonzalez-Gil, Ricardo; Gonzalez, Aida; Weyens, Nele; Lauga, Beatrice; Gallego, Jose Luis R.; Sanchez, Jesus; Isabel Pelaez, Ana

2017-01-01

The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica. The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonad...

Bacterial Structure and Characterization of Plant Growth Promoting and Oil Degrading Bacteria from the Rhizospheres of Mangrove Plants

NARCIS (Netherlands)

do Carmo, Flavia Lima; dos Santos, Henrique Fragoso; Martins, Edir Ferreira; van Elsas, Jan Dirk; Rosado, Alexandre Soares; Peixoto, Raquel Silva

Most oil from oceanic spills converges on coastal ecosystems, such as mangrove forests, which are threatened with worldwide disappearance. Particular bacteria that inhabit the rhizosphere of local plant species can stimulate plant development through various mechanisms; it would be advantageous if

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

Science.gov (United States)

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

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

OpenAIRE

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 no...

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

OpenAIRE

Susanne eSchreiter; Susanne eSchreiter; Guo-chun eDing; Guo-chun eDing; Holger eHeuer; Günter eNeumann; Martin eSandmann; Rita eGrosch; Siegfried eKropf; Kornelia eSmalla

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 ten years under the same agricultural management to reveal differences directly linked to the soil type and n...

Managing soil microbial communities in grain production systems through cropping practices

Science.gov (United States)

Gupta, Vadakattu

2013-04-01

Cropping practices can significantly influence the composition and activity of soil microbial communities with consequences to plant growth and production. Plant type can affect functional capacity of different groups of biota in the soil surrounding their roots, rhizosphere, influencing plant nutrition, beneficial symbioses, pests and diseases and overall plant health and crop production. The interaction between different players in the rhizosphere is due to the plethora of carbon and nutritional compounds, root-specific chemical signals and growth regulators that originate from the plant and are modulated by the physico-chemical properties of soils. A number of plant and environmental factors and management practices can influence the quantity and quality of rhizodeposition and in turn affect the composition of rhizosphere biota communities, microbe-fauna interactions and biological processes. Some of the examples of rhizosphere interactions that are currently considered important are: proliferation of plant and variety specific genera or groups of microbiota, induction of genes involved in symbiosis and virulence, promoter activity in biocontrol agents and genes correlated with root adhesion and border cell quality and quantity. The observation of variety-based differences in rhizodeposition and associated changes in rhizosphere microbial diversity and function suggests the possibility for the development of varieties with specific root-microbe interactions targeted for soil type and environment i.e. designer rhizospheres. Spatial location of microorganisms in the heterogeneous field soil matrix can have significant impacts on biological processes. Therefore, for rhizosphere research to be effective in variable seasonal climate and soil conditions, it must be evaluated in the field and within a farming systems context. With the current focus on security of food to feed the growing global populations through sustainable agricultural production systems there is a

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment

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Salvador eMirete

2015-10-01

Full Text Available Hypersaline environments are considered one of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes involved in salt resistance from the microbial communities of brines and the rhizosphere from the Es Trenc saltern (Mallorca, Spain. The microbial diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of communities that are typical in such environments. Metagenomic libraries from brine and rhizosphere samples, were transferred to the osmosensitive strain Escherichia coli MKH13, and screened for salt resistance. As a result, eleven genes that conferred salt resistance were identified, some encoding for well known proteins previously related to osmoadaptation as a glycerol and a proton pump, whereas others encoded for proteins not previously related to this function in microorganisms as DNA/RNA helicases, an endonuclease III (Nth and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and they also exhibited salt resistance in this bacterium, broadening the spectrum of bacterial species where these genes can operate. This is the first report of salt resistance genes recovered from metagenomes of a hypersaline environment.

Preliminary investigations of the rhizosphere nature of hydroponically grown lettuces

Science.gov (United States)

Antunes, Inês; Paille, Christel; Lasseur, Christophe

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

Volatile-mediated interactions in the rhizosphere

NARCIS (Netherlands)

Cordovez da Cunha, Viviane

2016-01-01

Plants and microorganisms are constantly engaged in highly dynamic interactions both above- and belowground. Several of these interactions are mediated by volatile organic compounds (VOCs), small carbon-based compounds with high vapor pressure at ambient temperature. In the rhizosphere, VOCs have

Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42.

Science.gov (United States)

Al-Ali, Ameen; Deravel, Jovana; Krier, François; Béchet, Max; Ongena, Marc; Jacques, Philippe

2017-10-23

In this work, the behavior in tomato rhizosphere of Bacillus velezensis FZB42 was analyzed taking into account the surfactin production, the use of tomato roots exudate as substrates, and the biofilm formation. B. velezensis FZB42 and B. amyloliquefaciens S499 have a similar capability to colonize tomato rhizosphere. Little difference in this colonization was observed with surfactin non producing B. velezensis FZB42 mutant strains. B. velezensis is able to grow in the presence of root exudate and used preferentially sucrose, maltose, glutamic, and malic acids as carbon sources. A mutant enable to produce exopolysaccharide (EPS - ) was constructed to demonstrate the main importance of biofilm formation on rhizosphere colonization. This mutant had completely lost its ability to form biofilm whatever the substrate present in the culture medium and was unable to efficiently colonize tomato rhizosphere.

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites

Czech Academy of Sciences Publication Activity Database

Elhottová, Dana; Krištůfek, Václav; Malý, S.; Frouz, Jan

2009-01-01

Roč. 40, 1-6 (2009), s. 758-770 ISSN 0010-3624 R&D Projects: GA MŠk LC06066; GA ČR GA526/03/1259 Institutional research plan: CEZ:AV0Z60660521 Keywords : colonizer plant * colliery spoil substrate * rhizosphere effect Subject RIV: EH - Ecology, Behaviour Impact factor: 0.397, year: 2009

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.

Science.gov (United States)

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.

PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response.

Science.gov (United States)

Hou, Jinyu; Liu, Wuxing; Wang, Beibei; Wang, Qingling; Luo, Yongming; Franks, Ashley E

2015-11-01

The aim of this study was to investigate petroleum phytoremediation enhancement by plant growth promoting bacteria (PGPR), specifically the correlation between petroleum hydrocarbon fractions and bacterial community structure affected by remediation and PGPR inocula. Aged petroleum contaminated soil was remediated by tall fescue (Testuca arundinacea L.) inoculated with two PGPR strains. Hydrocarbon degradation was measured by GC-MS (Gas-chromatography Mass-spectrometer) based on carbon fraction numbers (C8-C34). Changes in bacterial community structure were analyzed by high-throughput pyrosequencing of 16s rRNA. PGPR inoculation increased tall fescue biomass and petroleum hydrocarbons were removed in all the treatments. Maximum hydrocarbon removal, particular high molecular weight (C21-C34) aliphatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs), was observed in tall fescue inoculated with PGPR. The relative abundance of phyla γ-proteobacteria and Bacteroidetes increased after different treatments compared with controls. Moreover, a bacterial guild mainly comprising the genera Lysobacter, Pseudoxanthomonas, Planctomyces, Nocardioides, Hydrogenophaga, Ohtaekwangia was found to be positively correlated with C21-C34 petroleum hydrocarbons fractions removal by RDA analysis, implying that petroleum degradation was unrelated to bacterial community diversity but positively correlated with specific petroleum degraders and biosurfactant producers. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

OpenAIRE

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, ...

Dynamics of oxygen and carbon dioxide in rhizospheres of Lobelia dortmanna - a planar optode study of belowground gas exchange between plants and sediment.

Science.gov (United States)

Lenzewski, Nikola; Mueller, Peter; Meier, Robert Johannes; Liebsch, Gregor; Jensen, Kai; Koop-Jakobsen, Ketil

2018-04-01

Root-mediated CO 2 uptake, O 2 release and their effects on O 2 and CO 2 dynamics in the rhizosphere of Lobelia dortmanna were investigated. Novel planar optode technology, imaging CO 2 and O 2 distribution around single roots, provided insights into the spatiotemporal patterns of gas exchange between roots, sediment and microbial community. In light, O 2 release and CO 2 uptake were pronounced, resulting in a distinct oxygenated zone (radius: c. 3 mm) and a CO 2 -depleted zone (radius: c. 2 mm) around roots. Simultaneously, however, microbial CO 2 production was stimulated within a larger zone around the roots (radius: c. 10 mm). This gave rise to a distinct pattern with a CO 2 minimum at the root surface and a CO 2 maximum c. 2 mm away from the root. In darkness, CO 2 uptake ceased, and the CO 2 -depleted zone disappeared within 2 h. By contrast, the oxygenated root zone remained even after 8 h, but diminished markedly over time. A tight coupling between photosynthetic processes and the spatiotemporal dynamics of O 2 and CO 2 in the rhizosphere of Lobelia was demonstrated, and we suggest that O 2 -induced stimulation of the microbial community in the sediment increases the supply of inorganic carbon for photosynthesis by building up a CO 2 reservoir in the rhizosphere. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Spatial distribution of enzyme activities in the rhizosphere

Science.gov (United States)

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

2015-04-01

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

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

Science.gov (United States)

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

2015-01-01

The environmental stability of Tl-rich sphalerite in two contrasting soils was studied. Rhizospheric conditions were simulated to assess the risk associated with sulfide microparticles entering agricultural (top)soils. The data presented here clearly demonstrate a significant effect of 500 μM citric acid, a model rhizospheric solution, on ZnS alteration followed by enhanced Tl and Zn release. The relative ZnS mass loss after 28 days of citrate incubation reached 0.05 and 0.03 wt.% in Cambisol and Leptosol samples respectively, and was up to 4 times higher, compared to H2O treatments. Incongruent (i.e., substantially increased) mobilization of Tl from ZnS was observed during the incubation time. Generally higher (long-term) stability of ZnS with lower Tl release is predicted for soils enriched in carbonates. Furthermore, the important role of silicates (mainly illite) in the stabilization of mobilized Tl, linked with structural (inter)layer Tl-K exchange, is suggested. Thallium was highly bioavailable, as indicated by its uptake by white mustard; maximum Tl amounts were detected in biomass grown on the acidic Cambisol. Despite the fact that sulfides are thought as relatively stable phases in soil environments, enhanced sulfide dissolution and Tl/trace element release (and bioaccumulation) can be assumed in rhizosphere systems. Copyright © 2014 Elsevier B.V. All rights reserved.

Characterization of N-acylhomoserine lactone-degrading bacteria associated with the Zingiber officinale (ginger rhizosphere: Co-existence of quorum quenching and quorum sensing in Acinetobacter and Burkholderia

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Chhabra Siri

2011-03-01

Full Text Available Abstract Background Cell-to-cell communication (quorum sensing (QS co-ordinates bacterial behaviour at a population level. Consequently the behaviour of a natural multi-species community is likely to depend at least in part on co-existing QS and quorum quenching (QQ activities. Here we sought to discover novel N-acylhomoserine lactone (AHL-dependent QS and QQ strains by investigating a bacterial community associated with the rhizosphere of ginger (Zingiber officinale growing in the Malaysian rainforest. Results By using a basal growth medium containing N-(3-oxohexanoylhomoserine lactone (3-oxo-C6-HSL as the sole source of carbon and nitrogen, the ginger rhizosphere associated bacteria were enriched for strains with AHL-degrading capabilities. Three isolates belonging to the genera Acinetobacter (GG2, Burkholderia (GG4 and Klebsiella (Se14 were identified and selected for further study. Strains GG2 and Se14 exhibited the broadest spectrum of AHL-degrading activities via lactonolysis while GG4 reduced 3-oxo-AHLs to the corresponding 3-hydroxy compounds. In GG2 and GG4, QQ was found to co-exist with AHL-dependent QS and GG2 was shown to inactivate both self-generated and exogenously supplied AHLs. GG2, GG4 and Se14 were each able to attenuate virulence factor production in both human and plant pathogens. Conclusions Collectively our data show that ginger rhizosphere bacteria which make and degrade a wide range of AHLs are likely to play a collective role in determining the QS-dependent phenotype of a polymicrobial community.

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

Institute of Scientific and Technical Information of China (English)

SU Dechun; XING Jianping; JIAO Weiping; WONG Woonchung

2009-01-01

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

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

Science.gov (United States)

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.

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns

Science.gov (United States)

Creamer, Courtney A.; Filley, Timothy R.; Boutton, Thomas W.; Rowe, Helen I.

2016-06-01

Woodland encroachment into grasslands is a globally pervasive phenomenon attributed to land use change, fire suppression, and climate change. This vegetation shift impacts ecosystem services such as ground water allocation, carbon (C) and nutrient status of soils, aboveground and belowground biodiversity, and soil structure. We hypothesized that woodland encroachment would alter microbial community structure and function and would be related to patterns in soil C accumulation. To address this hypothesis, we measured the composition and δ13C values of soil microbial phospholipids (PLFAs) along successional chronosequences from C4-dominated grasslands to C3-dominated woodlands (small discrete clusters and larger groves) spanning up to 134 years. Woodland development increased microbial biomass, soil C and nitrogen (N) concentrations, and altered microbial community composition. The relative abundance of gram-negative bacteria (cy19:0) increased linearly with stand age, consistent with decreases in soil pH and/or greater rhizosphere development and corresponding increases in C inputs. δ13C values of all PLFAs decreased with time following woody encroachment, indicating assimilation of woodland C sources. Among the microbial groups, fungi and actinobacteria in woodland soils selectively assimilated grassland C to a greater extent than its contribution to bulk soil. Between the two woodland types, microbes in the groves incorporated relatively more of the relict C4-C than those in the clusters, potentially due to differences in below ground plant C allocation and organo-mineral association. Changes in plant productivity and C accessibility (rather than C chemistry) dictated microbial C utilization in this system in response to shrub encroachment.

Biofilm Formation and Indole-3-Acetic Acid Production by Two Rhizospheric Unicellular Cyanobacteria

NARCIS (Netherlands)

Ahmed, M.; Stal, L.J.; Hasnain, S.

2014-01-01

Microorganisms that live in the rhizosphere play a pivotal role in the functioning and maintenance of soil ecosystems. The study of rhizospheric cyanobacteria has been hampered by the difficulty to culture and maintain them in the laboratory. The present work investigated the production of the plant

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

NARCIS (Netherlands)

Ahmed, M.; Stal, L.J.; Hasnain, S.

2014-01-01

Microorganisms that live in the rhizosphere play a pivotal role in the functioning and maintenance of soil ecosystems. The study of rhizospheric cyanobacteria has been hampered by the difficulty to culture and maintain them in the laboratory. The present work investigated the production of the plant

Biodegradation of polycyclic aromatic hydrocarbons in rhizosphere soil

Energy Technology Data Exchange (ETDEWEB)

Schwab, A.P.; Banks, M.K.; Arunachalam, M. [Kansas State Univ., Manhattan, KS (United States)

1995-12-31

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

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

Science.gov (United States)

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.

Distribution of azotobacter in rhizosphere of maize

International Nuclear Information System (INIS)

Tahir, M.B.; Baig, M.B.

1998-01-01

Azotobacter distribution and species composition were studied under maize rhizosphere at four growth stages and in the uncropped soil (control). The study was conducted in the glazed pots with 10 kg soil in each pot. Soil in the pots was enriched with 20 mg N/kg and 15 mg/P/kg in the form of urea and single super phosphate, respectively. Six plants of maize variety Akbar were grown in 32 pots. Four pots were used as control (check). Sampling was done at four growth stages of 20, 40, 60 and 80 days after the germination of the crop. Results indicated that Azotobacter population increased as the plant growth progressed, reached maximum (1320) cells g/sup -1/ of soil at flowering stage and then declined. A chroococcum was found to be the dominant species in the main rhizosphere. (author)

Decrease of labile Zn and Cd in the rhizosphere of hyperaccumulating Thlaspi caerulescens with time

Energy Technology Data Exchange (ETDEWEB)

Dessureault-Rompre, Jacynthe, E-mail: dessureaultromj@agr.gc.c [Institute of Terrestrial Ecosystems (ITES), ETH Zurich, Universitaetstrasse 16, CH-8092 Zuerich (Switzerland); Luster, Joerg, E-mail: joerg.luster@wsl.c [Swiss Federal Institute for Forest, Snow, and Landscape Research (WSL), Zuercherstrasse 111, CH-8903 Birmensdorf (Switzerland); Schulin, Rainer, E-mail: rainer.schulin@env.ethz.c [Institute of Terrestrial Ecosystems (ITES), ETH Zurich, Universitaetstrasse 16, CH-8092 Zuerich (Switzerland); Tercier-Waeber, Mary-Lou, E-mail: marie-louise.tercier@unige.c [CABE, Department of Inorganic and Analytical Chemistry, Sciences II, University of Geneva, 30 quai Ernest Ansermet, CH-1211 Geneva 4 (Switzerland); Nowack, Bernd, E-mail: bernd.nowack@empa.c [Institute of Terrestrial Ecosystems (ITES), ETH Zurich, Universitaetstrasse 16, CH-8092 Zuerich (Switzerland); Empa - Swiss Federal Laboratories for Materials Testing and Research, Lerchenfeldstrasse 5, CH-9014 St. Gallen (Switzerland)

2010-05-15

By using a rhizobox micro-suction cup technique we studied in-situ mobilization and complexation of Zn and Cd in the rhizosphere of non-hyperaccumulating Thlaspi perfoliatum and two different Thlaspi caerulescens ecotypes, one of them hyperaccumulating Zn, the other Zn and Cd. The dynamic fraction (free metal ions and small labile complexes) of Zn and Cd decreased with time in the rhizosphere solution of the respective hyperaccumulating T. caerulescens ecotypes, and at the end of the experiment, it was significantly smaller than in the other treatments. Furthermore, the rhizosphere solutions of the T. caerulescens ecotypes exhibited a higher UV absorptivity than the solution of the T. perfoliatum rhizosphere and the plant-free soil. Based on our findings we suggest that mobile and labile metal-dissolved soil organic matter complexes play a key role in the rapid replenishment of available metal pools in the rhizosphere of hyperaccumulating T. caerulescens ecotypes, postulated earlier. - A mechanism that explains the rapid replenishment of metal pools accessible by hyperaccumulator plants for phytoextraction is proposed.

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

Science.gov (United States)

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

Decomposer biomass in the rhizosphere to assess rhizodeposition

DEFF Research Database (Denmark)

Christensen, Søren; Bjørnlund, Lisa; Madsen, Mette Vestergård

2007-01-01

under sterile conditions give an unrealistic value. Quantifying bacterial production from 3H-thymidine incorporation falls short in the rhizosphere and the use of isotopes does not allow clear distinction between labeled CO2 released from roots or microbes. We reduced rhizodeposition in 3-5 week old...... in the rhizosphere decreased to the level in soil unaffected by roots. This suggests that difference in bacterivore biomass directly reflects variations in rhizodeposition. Rhizodeposition is estimated from plant-induced increases in bacterial and bacterivore biomass, and yield factors, maintenance requirements......, and turnover rates from the literature. We use literature values that maximize requirements for organic carbon and still estimate the total organic rhizodeposition to be as little as 4-6% of the plant-induced respiration belowground....

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

KAUST Repository

Alzubaidy, Hanin S.; Essack, Magbubah; Malas, Tareq Majed Yasin; Bokhari, Ameerah; Motwalli, Olaa Amin; Kamanu, Frederick Kinyua; Jamhor, Suhaiza; Mokhtar, Noor Azlin; Antunes, Andre; Simoes, Marta; Alam, Intikhab; Bougouffa, Salim; Lafi, Feras Fawzi; Bajic, Vladimir B.; Archer, John A.C.

2015-01-01

To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

Science.gov (United States)

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

OpenAIRE

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

2013-01-01

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 greenh...

Biomass of active microorganisms is not limited only by available carbon in the rhizosphere

Science.gov (United States)

Gilmullina, Aliia

2017-04-01

Microbial activity is generally limited by carbon (C) availability. The easily available substrate release by roots creates so called "hotspots" in the rhizosphere that drives microbial activity removing C limitation. We simulated a gradient of root exudates by glucose addition at different concentrations to stimulate the activation of microbial biomass (MB). Glucose was added at the rates lower than MB (5, 10, 25 and 50%) and at the rates similar or higher than MB (100, 150, 200, 250, 300 and 400%). During incubation CO2 efflux was measured by conductometry, the size of active MB and specific growth rate were estimated by substrate-induced growth response method. We tested a hypothesis that glucose addition exceeding 100% MB is able to activate major fraction of soil microbial community. Addition of glucose at concentrations higher than 5% decreased specific growth rate, demonstrating the shift of microbial community from r-strategy to K-strategy. The percentage of active MB grew up by the increase of glucose concentration. The treatment with glucose at 100% presented a dramatic shift in the activation of MB up to 14%. Contrary to our hypothesis, further increase in glucose rate caused moderate stimulation of active MB up to 22% of total MB. Furthermore, glucose addition above 200% did not increase the fraction of active biomass indicating glucose oversaturation and possible limitation by other nutrients. The results suggest that despite the fact that C is the most important limitation factor, limitless C supply is not able to activate MB up to 100%. Thus, if the rhizosphere is limited by nutrients, the fraction of active biomass remains at low level despite an excess of available C.

Microbial degradation of trichloroethylene in the rhizosphere: Potential application to biological remediation of waste sites

International Nuclear Information System (INIS)

Walton, B.T.; Anderson, T.A.

1990-01-01

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

Atmospheric dinitrogen fixation in the flooded rhizosphere as determined by the N-15 isotope technique

International Nuclear Information System (INIS)

Yoshida, Tomio; Yoneyama, Tadakatsu.

1980-01-01

Atmospheric nitrogen fixation in the rice rhizosphere was determined under in situ conditions of growing flooded rice using the N-15 isotope method. The whole plant growing in a pot at a reproductive stage was placed in a specially designed glass container and exposed to a 15 N 2 atmosphere. The amounts of total nitrogen fixed in the rice rhizosphere under the experimental conditions were 1366, 592, 878, and 698 μg per pot containing 0.4 kg of soil during 15 N 2 exposure for 7 to 13 days in the four experiments conducted in this study. It was also found that the nitrogen fixed in the rice rhizosphere was translocated into other plant parts. Nineteen to 25% of the total atmospheric nitrogen fixed in the rice rhizosphere was found in the roots, leaves and stems, and ears of the rice plants during the 15 N 2 exposure period. (author)

Coupled Modeling of Rhizosphere and Reactive Transport Processes

Science.gov (United States)

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.

Effect of root exudates of various plants on composition of bacteria and fungi communities with special regard to pathogenic soil-borne fungi

OpenAIRE

Danuta Piętka; Elżbieta Patkowska

2013-01-01

The purpose of the studies conducted in the years 1996 - 1998 was to determine the composition of bacteria and fungi populations in the rhizosphere of winter wheat, spring wheat, soybean and potato, and in non-rhizosphere soil. Besides, the effect of root exudates of these plants on the formation of pathogenic fungi communities was established. The microbiological analysis showed that the greatest tolal number of bacteria was found in the rhizospheres of potato and soybean, and the lowest num...

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

Science.gov (United States)

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

2011-12-01

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

Nematode assemblages in the rhizosphere of spring barley (Hordeum vulgare L.) depended on fertilisation and plant growth phase

DEFF Research Database (Denmark)

Madsen, Mette Vestergård

2004-01-01

rhizosphere; nitrogen and phosphorus fertilisation; nematode assemblages; plant parasites; barley......rhizosphere; nitrogen and phosphorus fertilisation; nematode assemblages; plant parasites; barley...

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

Science.gov (United States)

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

Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert.

Science.gov (United States)

Řeháková, Klára; Chroňáková, Alica; Krištůfek, Václav; Kuchtová, Barbora; Čapková, Kateřina; Scharfen, Josef; Čapek, Petr; Doležal, Jiří

2015-01-01

Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies, and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m), in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters) on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter, and Paenibacillus, representing both r- and K-strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850-5000 m) and frost at the highest elevations (5750-5850 m). The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant T. ceaspitosum in a xeric environment and brings important information about

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment.

Science.gov (United States)

Bai, Yaohui; Huo, Yang; Liao, Kailingli; Qu, Jiuhui

2017-10-01

Traditional wastewater treatments based on activated sludge often encounter the problems of bulking and foaming, as well as malodor. To solve these problems, new treatment technologies have emerged in recent decades, including the ecological wastewater treatment process, which introduces selected local plants into the treatment system. With a focus on the underlying mechanisms of the ecological treatment process, we explored the microbial community biomass, composition, and function in the treatment system to understand the microbial growth in this system and its role in pollutant removal. Flow cytometry analysis revealed that ecological treatment significantly decreased influent bacterial quantity, with around 80% removal. 16S rRNA gene sequencing showed that the ecological treatment also altered the bacterial community structure of the wastewater, leading to a significant change in Comamonadaceae in the effluent. In the internal ecological system, because most of microbes aggregate in the plant rhizosphere and the sludge under plant roots, we selected two plant species (Nerium oleander and Arundo donax) to study the characteristics of rhizosphere and sludge microbes. Metagenomic results showed that the microbial community composition and function differed between the two species, and the microbial communities of A. donax were more sensitive to seasonal effects. Combined with their greater biomass and abundance of metabolic genes, microbes associated with N. oleander showed a greater contribution to pollutant removal. Further, the biodegradation pathways of some micropollutants, e.g., atrazine, were estimated.

Taxonomy of Streptomyces strains isolated from rhizospheres of ...

African Journals Online (AJOL)

Taxonomy of Streptomyces strains isolated from rhizospheres of various plant species grown in Taif region, KSA, having antagonistic activities against some microbial tissue ... African Journal of Biotechnology ... Keywords: Taxonomy, Streptomyces, microbial tissue culture contaminants, antagonistic activities, 16S rRNA

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

Science.gov (United States)

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.

Separating rhizosphere respiration from total soil respiration in two larch plantations in northeastern China.

Science.gov (United States)

Jiang, Lifen; Shi, Fuchen; Li, Bo; Luo, Yiqi; Chen, Jiquan; Chen, Jiakuan

2005-09-01

The potential capacity of soil to sequester carbon in response to global warming is strongly regulated by the ratio of rhizosphere respiration to respiration by soil microbial decomposers, because of their different temperature sensitivities. To quantify relative contributions of rhizosphere respiration to total soil respiration as influenced by forest stand development, we conducted a trenching study in two larch (Larix gmelini (Rupr.) Rupr.) plantations, aged 17 and 31 years, in northeastern China. Four plots in each plantation were randomly selected and trenched in early May 2001. Soil surface CO2 effluxes both inside and outside the plots were measured from May 2001 to August 2002. Soil respiration (i.e., the CO2 effluxes outside the trenched plots) varied similarly in the two plantations from 0.8 micromol m(-2) s(-1) in winter to 6.0 micromol m(-2) s(-1) in summer. Rhizosphere respiration (i.e., CO2 efflux outside the trenched plots minus that inside the plots) varied from 0.2 to 2.0 micromol m(-2) s(-1) in the old forest and from 0.3 to 4.0 micromol m(-2) s(-1) in the young forest over the seasons. Rhizosphere respiration, on average, accounted for 25% of soil respiration in the old forest and 65% in the young forest. Rhizosphere and soil respiration were significantly correlated with soil temperature but not with soil water content. We conclude that the role forests play in regulating climate change may depend on their age.

Plant uptake of radionuclides and rhizosphere factors

International Nuclear Information System (INIS)

Arie, Tsutomu; Gouthu, S.; Ambe, Shizuko; Yamaguchi, Isamu; Hirata, Hiroaki

1999-01-01

Influence of soil factors such as nuclide availability, pH, organic carbon, cation exchange capacity (CEC), exchangeable cations (Ca 2+ , Mg 2+ , and K + ), phosphate absorption coefficient (PAC), physical composition of soil (coarse sand, fine sand, silt, and clay), soil texture, and rhizosphere microbes on uptake of radionuclides by plants are studied. (author)

The effects of radial oxygen loss on arsenic tolerance and uptake in rice and on its rhizosphere

International Nuclear Information System (INIS)

Mei, X.Q.; Wong, M.H.; Yang, Y.; Dong, H.Y.; Qiu, R.L.; Ye, Z.H.

2012-01-01

Understanding the complex biotic and abiotic interactions invoked by the rice root system in oxygen-depleted soil is an important step in screening genotypes for low toxic metal or metalloid accumulation. A hydroponic and a rhizobox experiment have been conducted to explore the effects of varying root oxygen release on chemical changes, As fractionation in rhizosphere soil and Fe plaque formation, As uptake and tolerance by different rice genotypes. The results showed that rice genotypes with higher rates of radial oxygen loss (ROL) and at the bolting stage, tended to have greater effects on rhizosphere Eh, pH, Fe 3+ /Fe 2+ quotients, As fractionation and mobility and also on Fe plaque formation compared to those with lower ROL and at the tillering stage. Genotypes with higher ROL have a strong ability to reduce As accumulation in shoots and increase As tolerance by reducing As mobilization in the rhizosphere and by limiting As translocation. - Highlights: ► We investigate the effects of ROL on As tolerance, uptake, and changes in rhizosphere of rice genotypes and their correlation. ► Indices of As tolerance of genotypes are positively correlated with their rates of ROL. ► Genotypes with higher rates of ROL have greater effects on rhizosphere. ► Genotypes with higher rates of ROL have a strong ability to reduce As uptake by immobilizing As on roots and in rhizosphere. - Rice genotypes with high ROL and at the bolting stage have greater effects on their rhizosphere than others with lower ROL and at tillering stage and also have lower shoot As and higher As tolerance.

Plant diversity and plant identity influence Fusarium communities in soil.

Science.gov (United States)

LeBlanc, Nicholas; Kinkel, Linda; Kistler, H Corby

2017-01-01

Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics. Amplicon libraries targeting the RPB2 locus were generated from rhizosphere soil DNAs and sequenced using pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) and assigned a taxonomy using the Evolutionary Placement Algorithm. Fusarium community composition was differentiated between monoculture and polyculture plant communities, and by plant species in monoculture, but not in polyculture. Taxonomic classification of the Fusarium OTUs showed a predominance of F. tricinctum and F. oxysporum as well of the presence of a clade previously only found in the Southern Hemisphere. Total Fusarium richness was not affected by changes in plant community richness or correlated with soil physiochemical characteristics. However, OTU richness within two predominant phylogenetic lineages within the genus was positively or negatively correlated with soil physiochemical characteristics among samples within each lineage. This work shows that plant species, plant community richness, and soil physiochemical characteristics may all influence the composition and richness of Fusarium communities in soil.

Effects of different rhizosphere ventilation treatment on water and ...

African Journals Online (AJOL)

user

2011-02-07

environment of root soil, it alters rhizo- sphere ventilation, enhances the aerobic respiration, improves water and fertilizer absorption efficiency and redound water and nutrients' utilization. As to the effects of rhizosphere environment on ...

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

Science.gov (United States)

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

Plant uptake of radionuclides and rhizosphere factors

Energy Technology Data Exchange (ETDEWEB)

Arie, Tsutomu; Gouthu, S.; Ambe, Shizuko; Yamaguchi, Isamu [Institute of Physical and Chemical Research, Wako, Saitama (Japan); Hirata, Hiroaki

1999-03-01

Influence of soil factors such as nuclide availability, pH, organic carbon, cation exchange capacity (CEC), exchangeable cations (Ca{sup 2+}, Mg{sup 2+}, and K{sup +}), phosphate absorption coefficient (PAC), physical composition of soil (coarse sand, fine sand, silt, and clay), soil texture, and rhizosphere microbes on uptake of radionuclides by plants are studied. (author)

Cellular and molecular-genetic mechanisms of symbiosis and associative interaction of microorganisms with plants in rhizosphere

OpenAIRE

Lioshina L. G.

2009-01-01

The review contains the results of research on symbiotic and associative interaction of microorganisms and plants in rhizosphere. A special attention is given to the process of contact association of microorganisms and plants tissues including the concrete molecular structures and dominant role pertaining to protein-carbohydrate interaction. There are common features and distinctions at formation of arbuscular mycorhiza, rhizobia– legume symbiosis and association of non-leguminous plants with...

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

Science.gov (United States)

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.

Molecular Identification of Microorganisms Associated to the Rhizosphere of Vanilla Plants in Colombia

OpenAIRE

Claudia Lucía Álvarez López; Nelson Walter Osorio Vega; Mauricio Alejandro Marín Montoya

2013-01-01

The cultivation of vanilla (Vanilla planifolia) is highly promising in Colombia, but more research is needed on its agronomical management and beneficial microorganisms that grow associated to its rhizosphere, on which the plant depends for its nutrition and growth. This study involved the identification of microorganisms associated to the rhizosphere of vanilla plants in a crop located in Sopetrán, Colombia. The microbes were isolated in selective media for functional groups such as cellulol...

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

Energy Technology Data Exchange (ETDEWEB)

Kaplan, Daniel I., E-mail: daniel.kaplan@srnl.doe.gov [Savannah River National Laboratory, Aiken, SC 29808 (United States); Kukkadapu, Ravi [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 (United States); Seaman, John C. [Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802 (United States); Arey, Bruce W.; Dohnalkova, Alice C. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 (United States); Buettner, Shea [Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802 (United States); Li, Dien [Savannah River National Laboratory, Aiken, SC 29808 (United States); Varga, Tamas [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 (United States); Scheckel, Kirk G. [US Environmental Protection Agency, National Risk Management Research Laboratory, Cincinnati, OH 45224 (United States); Jaffé, Peter R. [Princeton University, Princeton, NJ 08540 (United States)

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 O{sub 2} 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. - Highlights: • Uranium concentrated in wetland environments • Hypothesized that plant roots change mineralogy and contaminant binding environment, promoting contaminant immobilization • Field study showed sharp dissolved U concentration profiles over the centimeter scale. • Spectroscopy identified unique mineralogy in rhizosphere compared to non-rhizosphere soil. • Uranium concentrated in root plaques in the + 6

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

International Nuclear Information System (INIS)

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.

2016-01-01

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 O_2 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. - Highlights: • Uranium concentrated in wetland environments • Hypothesized that plant roots change mineralogy and contaminant binding environment, promoting contaminant immobilization • Field study showed sharp dissolved U concentration profiles over the centimeter scale. • Spectroscopy identified unique mineralogy in rhizosphere compared to non-rhizosphere soil. • Uranium concentrated in root plaques in the + 6 oxidation

Effects of plant growth stage on the bioavailability of cesium and strontium in rhizosphere soil

International Nuclear Information System (INIS)

Nakamaru, Yasuo

2006-01-01

The effects of plant growth stage on the bioavailability of Cs and Sr in rhizosphere soil were studied by soybean pot experiments. Soybean seeds were sown into 12 pots and the plants were grown in a greenhouse for 84 d. Three pots were kept unplanted. The concentrations of Mg, K, Ca, Sr and Cs in plants and in soil solutions at different growth periods were measured. The mass flow of the elements from soil solution to the root surface was calculated from the concentrations in the soil solution and daily transpiration of the soybean plant. The concentrations of elements in the soil solution decreased as the soybean plants grew. The decrease of Mg, K, Ca, and Sr was high in planted pots. The differences in Mg, K, Ca, and Sr concentrations between the planted and the unplanted pots indicated that the active uptake of these elements by the soybean plants caused the drop in their concentrations. However, no obvious difference in Cs concentrations was seen between the planted and the unplanted ports. Although the ratio of mass flow to actual uptake of Cs was 1.4 for the vegetative growth stage, it increased to 4.2 for the podding stage. This meant that the Cs mass flow was in excess of what was absorbed by the plants, so the Cs uptake was inhibited near the roots for the podding stage. It was assumed that the increase of Cs sorption due to the K concentration decrease in soil solution decreased the Cs bioavailability in the rhizosphere soil. The bioavailability of Cs and Sr in the rhizosphere was examined in a small-scale pot experiment. The soil-soil solution distribution coefficients (K d ) of Cs and Sr were observed as an index of their sorption level. K d of Cs increased in the rhizosphere soil after cultivation. The decrease of bioavailable fraction of soil Cs was also observed. The exchangeable Cs in the rhizosphere soil clearly decreased. On the other hand, no specific rhizosphere effect was observed for Sr bioavailability. These results showed that the Cs

Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato

Science.gov (United States)

Antoniou, Anastasis; Tsolakidou, Maria-Dimitra; Stringlis, Ioannis A.; Pantelides, Iakovos S.

2017-01-01

Suppressive composts represent a sustainable approach to combat soilborne plant pathogens and an alternative to the ineffective chemical fungicides used against those. Nevertheless, suppressiveness to plant pathogens and reliability of composts are often inconsistent with unpredictable effects. While suppressiveness is usually attributed to the compost’s microorganisms, the mechanisms governing microbial recruitment by the roots and the composition of selected microbial communities are not fully elucidated. Herein, the purpose of the study was to evaluate the impact of a compost on tomato plant growth and its suppressiveness against Fusarium oxysporum f. sp. lycopersici (Foxl) and Verticillium dahliae (Vd). First, growth parameters of tomato plants grown in sterile peat-based substrates including 20 and 30% sterile compost (80P/20C-ST and 70P/30C-ST) or non-sterile compost (80P/20C and 70P/30C) were evaluated in a growth room experiment. Plant height, total leaf surface, and fresh and dry weight of plants grown in the non-sterile compost mixes were increased compared to the plants grown in the sterile compost substrates, indicating the plant growth promoting activity of the compost’s microorganisms. Subsequently, compost’s suppressiveness against Foxl and Vd was evaluated with pathogenicity experiments on tomato plants grown in 70P/30C-ST and 70P/30C substrates. Disease intensity was significantly less in plants grown in the non-sterile compost than in those grown in the sterile compost substrate; AUDPC was 2.3- and 1.4-fold less for Foxl and Vd, respectively. Moreover, fungal quantification in planta demonstrated reduced colonization in plants grown in the non-sterile mixture. To further investigate these findings, we characterized the culturable microbiome attracted by the roots compared to the unplanted compost. Bacteria and fungi isolated from unplanted compost and the rhizosphere of plants were sequence-identified. Community-level analysis revealed

Co-existence of Rhizobia and Diverse Non-rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii, Rhizobium multihospitium–Like and Burkholderia pyrrocinia–Like Strains

Directory of Open Access Journals (Sweden)

Junkun Lu

2017-11-01

Full Text Available Rhizobia induce root nodules and fix atmospheric N2 for most legume species in exchange for carbon. However, the diverse endophytic non-rhizobial bacteria in legume nodules that co-exist with rhizobia are often ignored because they are difficult to cultivate using routine cultivation approaches. To enhance our understanding of the incidence and diversity of legume–bacteria associations, a high-throughput sequencing analysis of bacterial 16S rRNA genes was used to examine the bacterial community in the rhizospheres and root nodules of Dalbergia odorifera seedlings that were uninoculated or inoculated with Bradyrhizobium elkanii H255, Rhizobium multihospitium–like HT221, or Burkholderia pyrrocinia–like H022238, in two growth media (nitrogen [N]-supplied soil or N-omitted potting mix. Seedlings inoculated with Bradyrhizobium had significantly more nodules than seedlings in the other inoculation conditions, regardless of growth media. Using the 15N natural abundance method, it was shown that the inoculated plants had significantly higher N2 fixation efficiency (48–57% and specific nodule activity [269–313 μg N mg−1 of dry weight (dwt nodule] compared to the uninoculated plants (203 μg N mg−1 dwt nodule. The 16S rRNA gene analysis showed that there was generally a higher bacterial diversity in the rhizosphere than in the nodules in the corresponding condition. Both rhizobial inoculation and media status significantly altered the bacterial communities in the rhizospheres and nodules (P < 0.05, with the exception of the inoculated soil rhizospheres. Regarding non-rhizobial bacteria, three genera, i.e., Lactococcus, Bacillus, and Pseudomonas, were consistently enriched in the rhizosphere and Bradyrhizobium, Chloroplast norank (which belongs to Cyanobacteria, and Lactococcus were commonly found in the nodules. In contrast, common rhizobial genera (including Rhizobium, Mesorhizobium, and Burkholderia were only present in the nodules at low

in vitro screening of selected herbicides on rhizosphere mycoflora

African Journals Online (AJOL)

PROF. BARTH EKWEME

inhibited the mycelial growth of the isolated rhizosphere fungi. Growth inhibition of the ... quality of crops but also utilize essential nutrients meant for the crop. ..... Effect of seed-applied pesticide on growth ... soil fungi from oil palm plantation.

Copper availability and bioavailability are controlled by rhizosphere pH in rape grown in an acidic Cu-contaminated soil

International Nuclear Information System (INIS)

Chaignon, Valerie; Quesnoit, Marie; Hinsinger, Philippe

2009-01-01

We evaluated how root-induced changes in rhizosphere pH varied and interacted with Cu availability and bioavailability in an acidic soil. Rape was grown on a Cu-contaminated acidic soil, which had been limed at 10 rates. Soil Cu bioavailability was not influenced by liming. However, liming significantly decreased CaCl 2 -extracted Cu for pH between 3.7 and 5.1. Little effect was found for pH above 5.1. For soil pH 2 -Cu contents were smaller in rhizosphere than uncropped soil. Rhizosphere alkalisation occurred at pH 2 -Cu in the rhizosphere at low pH and the absence of pH dependency of Cu bioavailability to rape. In addition, apoplastic Cu in roots increased with increasing soil pH, most probably as a result of increased dissociation and affinity of cell wall compounds for Cu. - Root-induced increase in pH reduces Cu availability in the rhizosphere and Cu bioavailability to rape.

Rhizosphere bacterial diversity and heavy metal accumulation in Nymphaea pubescens in aid of phytoremediation potential

Directory of Open Access Journals (Sweden)

RAISA KABEER

2014-04-01

Full Text Available The present work aims to characterize the bacterial diversity of the rhizosphere system of Nymphaea pubescens and the sediment system where it grows naturally. Heavy metal content in the sediment and Nymphea plant from the selected wetland system were also studied. Results of the current study showed that the concentration of copper, zinc and lead in the sediment ranged from 43 to 182 mg/Kg, from 331 to 1382 mg/Kg and from 121 to 1253 mg/Kg, respectively. Cadmium concentration in sediment samples was found to be zero and the order of abundance of heavy metals in the sediment samples was Zn>Pb>Cu>Cd. The abundance patterns of heavy metals in leaf, petiole and root were Cd>Cu>Pb>Zn. Microbial load in rhizosphere of Nymphea pubescens ranged from 93×102 to 69×103 and that of sediment was 62×102 to 125×103. Bacterial load in rhizosphere was higher than that of growing sediment. Four bacterial genera were identified from the rhizosphere of Nymphaea pubescens which include Acinetobacter, Alcaligens, Listeria and Staphylococcus. Acinetobacter, Alcaligens and Listeria are the three bacterial genera isolated from sediment samples. Copper resistance studies of the 14 bacterial isolates from rhizosphere and 7 strains from sediment samples revealed that most of them showed low resistance (<100 μg/ml and very few isolates showed high resistance of 400-500 μg/ml.

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

Science.gov (United States)

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.

An evolving network model with community structure

International Nuclear Information System (INIS)

Li Chunguang; Maini, Philip K

2005-01-01

Many social and biological networks consist of communities-groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting community structures in real-world complex networks. In this paper, we propose an evolving network model which exhibits community structure. The network model is based on the inner-community preferential attachment and inter-community preferential attachment mechanisms. The degree distributions of this network model are analysed based on a mean-field method. Theoretical results and numerical simulations indicate that this network model has community structure and scale-free properties

Data on rhizosphere pH, phosphorus uptake and wheat growth responses upon TiO2 nanoparticles application

Directory of Open Access Journals (Sweden)

Rafia Rafique

2018-04-01

Full Text Available In this study, the data sets and analyses provided the information on the characterization of titanium dioxide nanoparticles (TiO2 NPs, and their impacts on rhizosphere pH, and soil-bound phosphorus (P availability to plants together with relevant parameters. For this purpose, wheat (Triticum aestivum L. was cultivated in the TiO2 NPs amended soil over a period of 60 days. After harvesting, the soil and plants were analyzed to examine the rhizosphere pH, P availability in rhizosphere soil, uptake in roots and shoots, biomass produced, chlorophyll content and translocation to different plant parts monitored by SEM and EDX techniques in response to different dosages of TiO2 NPs. The strong relationship can be found among TiO2 NPs application, P availability, and plant growth. Keywords: Rhizosphere pH, TiO2 NPs nanoparticles, Wheat, Phosphorus, Uptake

Cellular and molecular-genetic mechanisms of symbiosis and associative interaction of microorganisms with plants in rhizosphere

Directory of Open Access Journals (Sweden)

Lioshina L. G.

2009-02-01

Full Text Available The review contains the results of research on symbiotic and associative interaction of microorganisms and plants in rhizosphere. A special attention is given to the process of contact association of microorganisms and plants tissues including the concrete molecular structures and dominant role pertaining to protein-carbohydrate interaction. There are common features and distinctions at formation of arbuscular mycorhiza, rhizobia– legume symbiosis and association of non-leguminous plants with Azospirillum

Secondary Structural Models (16S rRNA of Polyhydroxyalkanoates Producing Bacillus Species Isolated from Different Rhizospheric Soil: Phylogenetics and Chemical Analysis

Directory of Open Access Journals (Sweden)

Swati Mohapatra

2016-09-01

Full Text Available Polyhydroxyalkanoates (PHAs producing bacterial isolates are gaining more importance over the world due to the synthesis of a biodegradable polymer which is extremely desirable to substitute synthetic plastics. PHAs are produced by various microorganisms under certain stress conditions. In this study, sixteen bacterial isolates characterized previously by partial 16S rRNA gene sequencing (NCBI Accession No. KF626466 to KF626481 were again stained by Nile red after three years of preservation in order to confirm their ability to accumulate PHAs. Also, phylogenetic analysis carried out in the present investigation evidenced that the bacterial species belonging to genus Bacillus are the dominant flora of the rhizospheric region, with a potentiality of biodegradable polymer (PHAs production. Again, RNA secondary structure prediction hypothesized that there is no direct correlation between RNA folding pattern stability with a rate of PHAs production among the selected isolates of genus Bacillus.

Molecular identification of microorganisms associated to the rhizosphere of vanilla plants in Colombia

International Nuclear Information System (INIS)

Alvarez Lopez, Claudia Lucia; Osorio Vega, Nelson Walter; Marin Montoya, Mauricio Alejandro

2013-01-01

The cultivation of vanilla (Vanilla planifolia) is highly promising in Colombia, but more research is needed on its agronomical management and beneficial microorganisms that grow associated to its rhizosphere, on which the plant depends for its nutrition and growth. This study involved the identification of microorganisms associated to the rhizosphere of vanilla plants in a crop located in Sopetran, Colombia. The microbes were isolated in selective media for functional groups such as cellulolytic, proteolytic, inorganic and organic phosphate (phytate) solubilizers, and asymbiotic nitrogen fixing bacteria. After isolation and purification, 109 microbial isolates were obtained. DNA was extracted from 52 selected isolates for molecular identification based on its and 16s RDNA sequencing, for fungi and bacteria, respectively. The diversity of rhizosphere microorganisms found was significant. Bacteria such as Bacillus Megaterium, Pseudomonas koreensis and Acinetobacter sp., and the Fungus Plectosphaerella sp., may have a high potential to be used as biofertilizers to improve vanilla plant nutrition and growth.

Dissipation of polycyclic aromatic hydrocarbons (PAHs) in the rhizosphere: Synthesis through meta-analysis

International Nuclear Information System (INIS)

Ma Bin; He Yan; Chen Huaihai; Xu Jianming; Rengel, Zed

2010-01-01

Polycyclic aromatic hydrocarbons (PAHs) are widespread and persistent organic pollutants with high carcinogenic effect and toxicity; their behavior and fate in the soil-plant system have been widely investigated. In the present paper, meta-analysis was used to explore the interaction between plant growth and dissipation of PAHs in soil based on the large body of published literature. Plants have a promoting effect on PAH dissipation in soils. There was no difference in PAH dissipation between soils contaminated with single and mixed PAHs. However, plants had a more obvious effect on PAH dissipation in freshly-spiked soils than in long-term field-polluted soils. Additionally, a positive effect of the number of microbial populations capable of degrading PAHs was observed in the rhizosphere compared with the bulk soil. Our meta-analysis established the importance of the rhizosphere effect on PAH dissipation in variety of the soil-plant systems. - The meta-analysis provides the first quantitative evidence of the positive effect of rhizosphere processes on PAH dissipation.

The overlapping community structure of structural brain network in young healthy individuals.

Directory of Open Access Journals (Sweden)

Kai Wu

2011-05-01

Full Text Available Community structure is a universal and significant feature of many complex networks in biology, society, and economics. Community structure has also been revealed in human brain structural and functional networks in previous studies. However, communities overlap and share many edges and nodes. Uncovering the overlapping community structure of complex networks remains largely unknown in human brain networks. Here, using regional gray matter volume, we investigated the structural brain network among 90 brain regions (according to a predefined anatomical atlas in 462 young, healthy individuals. Overlapped nodes between communities were defined by assuming that nodes (brain regions can belong to more than one community. We demonstrated that 90 brain regions were organized into 5 overlapping communities associated with several well-known brain systems, such as the auditory/language, visuospatial, emotion, decision-making, social, control of action, memory/learning, and visual systems. The overlapped nodes were mostly involved in an inferior-posterior pattern and were primarily related to auditory and visual perception. The overlapped nodes were mainly attributed to brain regions with higher node degrees and nodal efficiency and played a pivotal role in the flow of information through the structural brain network. Our results revealed fuzzy boundaries between communities by identifying overlapped nodes and provided new insights into the understanding of the relationship between the structure and function of the human brain. This study provides the first report of the overlapping community structure of the structural network of the human brain.

Rhizosphere soil microbial index of tree species in a coal mining ecosystem

Energy Technology Data Exchange (ETDEWEB)

Sinha, S.; Masto, R.E.; Ram, L.C.; Selvi, V.A.; Srivastava, N.K.; Tripathi, R.C.; George, J. [Central Institute of Mining & Fuel Research, Dhanbad (India)

2009-09-15

Microbial characterization of the tree rhizosphere provides important information relating to the screening of tree species for re-vegetation of degraded land. Rhizosphere soil samples collected from a few predominant tree species growing in the coal mining ecosystem of Dhanbad, India, were analyzed for soil organic carbon (SOC), mineralizable N, microbial biomass carbon (MBC), active microbial biomass carbon (AMBC), basal soil respiration (BSR), and soil enzyme activities (dehydrogenase, urease, catalase, phenol oxidase, and peroxidase). Principal component analysis was employed to derive a rhizosphere soil microbial index (RSMI) and accordingly, dehydrogenase, BSR/MBC, MBC/SOC, EC, phenol oxidase and AMBC were found to be the most critical properties. The observed values for the above properties were converted into a unitless score (0-1.00) and the scores were integrated into RSMI. The tree species could be arranged in decreasing order of the RSMI as: A. marmelos (0.718), A. indica (0.715), Bauhinia bauhinia (0.693), B. monosperma (0.611), E. jambolana (0.601), Moringa oleifera (0.565), Dalbergia sissoo (0.498), T indica (0.488), Morus alba (0.415), F religiosa (0.291), Eucalyptus sp. (0.232) and T grandis (0.181). It was concluded that tree species in coal mining areas had diverse effects on their respective rhizosphere microbial processes, which could directly or indirectly determine the survival and performance of the planted tree species in degraded coal mining areas. Tree species with higher RSMI values could be recommended for re-vegetation of degraded coal mining area.

Afforestation alters community structure of soil fungi.

Science.gov (United States)

Carson, Jennifer K; Gleeson, Deirdre B; Clipson, Nicholas; Murphy, Daniel V

2010-07-01

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

Science.gov (United States)

Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

2017-12-19

Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

Epidemic spreading on complex networks with community structures

NARCIS (Netherlands)

Stegehuis, C.; van der Hofstad, R.W.; van Leeuwaarden, J.S.H.

2016-01-01

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities

Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon-contaminated and uncontaminated soils following willow (Salix spp. L. planting.

Directory of Open Access Journals (Sweden)

Saad El-Din Hassan

Full Text Available Phytoremediation is a potentially inexpensive alternative to chemical treatment of hydrocarbon-contaminated soils, but its success depends heavily on identifying factors that govern the success of root-associated microorganisms involved in hydrocarbon degradation and plant growth stimulation. Arbuscular mycorrhizal fungi (AMF form symbioses with many terrestrial plants, and are known to stimulate plant growth, although both species identity and the environment influence this relationship. Although AMF are suspected to play a role in plant adaptation to hydrocarbon contamination, their distribution in hydrocarbon-contaminated soils is not well known. In this study, we examined how AMF communities were structured within the rhizosphere of 11 introduced willow cultivars as well as unplanted controls across uncontaminated and hydrocarbon-contaminated soils at the site of a former petrochemical plant. We obtained 69 282 AMF-specific 18S rDNA sequences using 454-pyrosequencing, representing 27 OTUs. Contaminant concentration was the major influence on AMF community structure, with different AMF families dominating at each contaminant level. The most abundant operational taxonomic unit in each sample represented a large proportion of the total community, and this proportion was positively associated with increasing contamination, and seemingly, by planting as well. The most contaminated soils were dominated by three phylotypes closely related to Rhizophagus irregularis, while these OTUs represented only a small proportion of sequences in uncontaminated and moderately contaminated soils. These results suggest that in situ inoculation of AMF strains could be an important component of phytoremediation treatments, but that strains should be selected from the narrow group that is both adapted to contaminant toxicity and able to compete with indigenous AMF species.

Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon-contaminated and uncontaminated soils following willow (Salix spp. L.) planting.

Science.gov (United States)

Hassan, Saad El-Din; Bell, Terrence H; Stefani, Franck O P; Denis, David; Hijri, Mohamed; St-Arnaud, Marc

2014-01-01

Phytoremediation is a potentially inexpensive alternative to chemical treatment of hydrocarbon-contaminated soils, but its success depends heavily on identifying factors that govern the success of root-associated microorganisms involved in hydrocarbon degradation and plant growth stimulation. Arbuscular mycorrhizal fungi (AMF) form symbioses with many terrestrial plants, and are known to stimulate plant growth, although both species identity and the environment influence this relationship. Although AMF are suspected to play a role in plant adaptation to hydrocarbon contamination, their distribution in hydrocarbon-contaminated soils is not well known. In this study, we examined how AMF communities were structured within the rhizosphere of 11 introduced willow cultivars as well as unplanted controls across uncontaminated and hydrocarbon-contaminated soils at the site of a former petrochemical plant. We obtained 69 282 AMF-specific 18S rDNA sequences using 454-pyrosequencing, representing 27 OTUs. Contaminant concentration was the major influence on AMF community structure, with different AMF families dominating at each contaminant level. The most abundant operational taxonomic unit in each sample represented a large proportion of the total community, and this proportion was positively associated with increasing contamination, and seemingly, by planting as well. The most contaminated soils were dominated by three phylotypes closely related to Rhizophagus irregularis, while these OTUs represented only a small proportion of sequences in uncontaminated and moderately contaminated soils. These results suggest that in situ inoculation of AMF strains could be an important component of phytoremediation treatments, but that strains should be selected from the narrow group that is both adapted to contaminant toxicity and able to compete with indigenous AMF species.

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

Science.gov (United States)

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

Science.gov (United States)

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...

[Correlation between distribution of rhizospheric microorganisms and contents of steroidal saponins of Paris polyphylla var. yunnanensis].

Science.gov (United States)

Zhou, Nong; Qi, Wen-hua; Xiao, Guo-sheng; Ding, Bo; Zhang, Hua; Guo, Dong-qin; Shen, Wei

2015-03-01

In this paper, the varying pattern of the amount of rhizospheric microorganisms, including bacteria, actinomycetes and fungus, was observed during the cultivation of Paris polyphylla var. yunnanensis. And the correlations between number of rhizospheric microorganisms and the quality of P. polyphylla var. yunnanensis were also studied. The results showed that the rhizospheric microorganism source of P. polyphylla var. yunnanensis was rich. The distribution of rhizospheric microorganisms (soil bacteria, fungus, actinomycetes, potassium-solubilizing bacteria, inorganic phosphorus-solubilizing bacteria, organic phosphorus-solubilizing bacteria) collected from different origin places existed significant difference (P the amount of actinomycetes > the amount of fungus. The medicinal quality of P. polyphylla var. yunnanensis was influenced by their habits, and the increase of cultivation years caused the obvious decrease of the quality of P. polyphylla var. yunnanensis. Therefore, the increase of cultivation years will cause the variation of the soil micro-ecology flora, and decrease the nutrient absorption and the utilization of P. polyphylla var. yunnanensis, which will make the decrease of the medical quality of P. polyphylla var. yunnanensis.

Copper availability and bioavailability are controlled by rhizosphere pH in rape grown in an acidic Cu-contaminated soil

Energy Technology Data Exchange (ETDEWEB)

Chaignon, Valerie; Quesnoit, Marie [INRA, UMR 1222 Eco and Sols Ecologie fonctionnelle and Biogeochimie des Sols (INRA-IRD-SupAgro), Place Viala, F-34060 Montpellier (France); Hinsinger, Philippe, E-mail: philippe.hinsinger@supagro.inra.f [INRA, UMR 1222 Eco and Sols Ecologie fonctionnelle and Biogeochimie des Sols (INRA-IRD-SupAgro), Place Viala, F-34060 Montpellier (France)

2009-12-15

We evaluated how root-induced changes in rhizosphere pH varied and interacted with Cu availability and bioavailability in an acidic soil. Rape was grown on a Cu-contaminated acidic soil, which had been limed at 10 rates. Soil Cu bioavailability was not influenced by liming. However, liming significantly decreased CaCl{sub 2}-extracted Cu for pH between 3.7 and 5.1. Little effect was found for pH above 5.1. For soil pH < 4.4, CaCl{sub 2}-Cu contents were smaller in rhizosphere than uncropped soil. Rhizosphere alkalisation occurred at pH < 4.8, while acidification occurred at greater pH. This explained the changes of CaCl{sub 2}-Cu in the rhizosphere at low pH and the absence of pH dependency of Cu bioavailability to rape. In addition, apoplastic Cu in roots increased with increasing soil pH, most probably as a result of increased dissociation and affinity of cell wall compounds for Cu. - Root-induced increase in pH reduces Cu availability in the rhizosphere and Cu bioavailability to rape.

Effects of pre- and post-transplant inoculation with commercial arbuscular mycorrhizal (AM fungi on pelargonium (Pelargonium hortorum and its microorganism community

Directory of Open Access Journals (Sweden)

Gergely Csima

2012-03-01

Full Text Available Rooted cuttings of geranium were grown with and without a slow release fertilizer and inoculated or not with a commercial inoculum containing AM fungi. After six weeks plants were transplanted into larger containers and one-half of the plants were inoculated with AM. Inoculation increased pelargonium growth along with nitrogen, phosphorous and potassium concentrations in shoot than caused a slight decrease in shoot growth and enhanced N concentration. Colony forming units of total fungi and bacteria in the rhizosphere were not influenced by AM;  although RFLP profiles of DNA isolated from bacteria living in rhizosphere showed a more diverse community in AM-inoculated than non-inoculated plants at low nutrient supply. Our results suggest that mycorrhizal inoculation not only has an effect on plant growth and uptake of elements but it also influences directly or indirectly the bacterial community of the rhizosphere.

小麦/玉米/大豆和小麦/玉米/甘薯套作对根际土壤细菌群落多样性及植株氮素吸收的影响%Effect of Wheat/Maize/Soybean and Wheat/Maize/Sweet Potato Relay Strip Intercropping on Bacterial Community Diversity of Rhizosphere Soil and Nitrogen Uptake of Crops

Institute of Scientific and Technical Information of China (English)

雍太文; 杨文钰; 向达兵; 朱贞颖

2012-01-01

为探讨小麦/玉米/大豆和小麦/玉米/甘薯套作体系中根际细菌群落多样性与作物氮素高效吸收的差异特性及二者间的关系,应用变性梯度凝胶电泳(DGGE)技术研究了小麦-大豆(A1)、小麦-甘薯(A2)、玉米(A3)、小麦/玉米/大豆(A4)和小麦/玉米/甘薯(A5)5种种植模式的根际细菌群落多样性.结果表明,与A1、A2、A3及A5相比,A4套作提高了各作物在开花期(或吐丝期)与成熟期的籽粒吸氮量、地上部总吸氮量和Shannon-Weiner index多样性指数(H′).处理间的吸氮量与H′的变化规律为套作＞单作、大豆茬口＞甘薯茬口,以A4处理最高.不同种植模式下DGGE图谱条带的数量及亮度有较大区别,且有几条特征性条带发生了明显变化.不同种植模式间的细菌群落结构相似性较低,群落相似度系数(Cs)表现为套作与套作间＞套作与单作间；A4与A5间的Cs相对较小,二者间的细菌群落结构差异较大.A4模式有利于提高根际细菌群落多样性,增强植株对氮素的吸收能力.%The aim of this study was to understand the relationship between diversity of rhizosphere bacterial community and nitrogen uptake of crops in two relay strip intercropping systems: wheat/maize/soybean and wheat/maize/sweet potato. We analyzed the diversities of rhizosphere bacterial community in five cropping systems using denaturing gradient gel electrophoresis (DGGE) based on 16S rDNA. The cropping systems included wheat-soybean (Al), wheat-sweet potato (A2), maize single cropping (A3), wheat/maize/soybean (A4), and wheat/maize/sweet potato (A5). Compared to the sole cropping systems (Al, A2, and A3 treatments), the A4 treatment showed increases in grain nitrogen uptake and total nitrogen uptake amounts of aboveground of crops at both flowering (or silking) and maturity stages, and the Shannon-Weiner indices for rhizosphere bacterial community diversity was also increased significantly. The values of nitrogen

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

Science.gov (United States)

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.

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii)

Science.gov (United States)

Li, Qiang; Zhao, Jian; Xiong, Chuan; Li, Xiaolin; Chen, Zuqin; Li, Ping; Huang, Wenli

2017-01-01

The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum. PMID:28410376

Changes in Actinomycetes community structure under the influence of Bt transgenic brinjal crop in a tropical agroecosystem.

Science.gov (United States)

Singh, Amit Kishore; Singh, Major; Dubey, Suresh Kumar

2013-05-29

The global area under brinjal cultivation is expected to be 1.85 million hectare with total fruit production about 32 million metric tons (MTs). Brinjal cultivars are susceptible to a variety of stresses that significantly limit productivity. The most important biotic stress is caused by the Brinjal fruit and shoot Borer (FSB) forcing farmers to deploy high doses of insecticides; a matter of serious health concern. Therefore, to control the adverse effect of insecticides on the environment including the soil, transgenic technology has emerged as the effective alternative. However, the reports, regarding the nature of interaction of transgenic crops with the native microbial community are inconsistent. The effect of a Bt transgenic brinjal expressing the bio-insecticidal protein (Cry1Ac) on the rhizospheric community of actinomycetes has been assessed and compared with its non-transgenic counterpart. Significant variation in the organic carbon observed between the crops (non-Bt and Bt brinjal) may be due to changes in root exudates quality and composition mediated by genetic attributes of Bt transgenic brinjal. Real time quantitative PCR indicated significant differences in the actinomycetes- specific 16S rRNA gene copy numbers between the non-Bt (5.62-27.86) × 1011 g-1 dws and Bt brinjal planted soil (5.62-24.04) × 1011 g-1 dws. Phylogenetic analysis indicated 14 and 11, actinomycetes related groups in soil with non-Bt and Bt brinjal crop, respectively. Micrococaceaea and Nocardiodaceae were the dominant groups in pre-vegetation, branching, flowering, maturation and post-harvest stage. However, Promicromonosporaceae, Streptosporangiaceae, Mycobacteriaceae, Geodermatophilaceae, Frankiaceae, Kineosporaceae, Actisymmetaceae and Streptomycetaceae were exclusively detected in a few stages in non-Bt brinjal rhizosphere soil while Nakamurellaceae, Corynebactericeae, Thermomonosporaceae and Pseudonocardiaceae in Bt brinjal counterpart. Field trails envisage

Habitat constraints on the functional significance of soil microbial communities

Science.gov (United States)

Nunan, Naoise; Leloup, Julie; Ruamps, Léo; Pouteau, Valérie; Chenu, Claire

2017-04-01

An underlying assumption of most ecosystem models is that soil microbial communities are functionally equivalent; in other words, that microbial activity under given set of conditions is not dependent on the composition or diversity of the communities. Although a number of studies have suggested that this assumption is incorrect, ecosystem models can adequately describe ecosystem processes, such as soil C dynamics, without an explicit description of microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that microbial communities are not always functionally equivalent. The data suggest that when the supply of substrate is restricted, then the functioning of different microbial communities cannot be distinguished, but when the supply is less restricted, the intrinsic functional differences among communities can be expressed. When the supply of C is restricted then C dynamics are related to the properties of the physical and chemical environment of the soil. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments such as the rhizosphere or the litter layer, but are less likely to do so in oligotrophic environments such as the mineral layers of soil.

Microbial diversity and metagenomic analysis of the rhizosphere of para grass (Urochloa mutica) growing under saline conditions

International Nuclear Information System (INIS)

Mukhtar, S.; Awan, H. A.; Maqbool, A.; Mehnaz, S.; Malik, K. A.

2016-01-01

Para grass is a salt tolerant plant, grown on salt affected soils of Punjab, Pakistan. The aim of this study was to investigate the distribution of culturable and non-culturable bacteria in the rhizosphere, rhizoplane and histoplane of para grass, growing under saline conditions. A total of seventy four, bacterial strains were isolated and characterized. Among these, thirty two from rhizosphere, twenty two from rhizoplane and twenty were from the histoplane. Cultureable bacteria were characterized by biochemical tests and 16S rRNA gene sequence analysis. Non-culturable bacteria were identified by PCR amplification of 16S rRNA gene, using metagenomic approach. Seventy seven percent bacterial isolates from rhizosphere and rhizoplane fractions were identified as member of Proteobacteria. Twenty five percent isolates of histoplane fraction were members of firmicutes while 68.75 percent were of Proteobacteria. Of total isolates, 50 percent could grow in nitrogen free medium and 21.67 percent on halophilic medium. Nitrogen fixers and halophilic bacteria were more abundant in the rhizosphere as compared to roots. 16S rRNA gene clone library analysis showed that out of 48 clones, 14 were uncultured, classified; eighteen un-cultured un-classified, while others related to 16 different known cultured groups of bacteria. Results for cultured and uncultured bacteria revealed a wide diversity of bacterial population present in the rhizosphere of para grass. (author)

Heavy Metal Content and Microbial Composition of the Rhizosphere ...

African Journals Online (AJOL)

Plant-assisted bioremediation holds promise for in-situ treatment of polluted soil. However, en-hancement of this process for successful phytoremediation processes requires a sound understand-ing of the complex interactions of the rhizosphere. The present study thus investigated the chemi-cal and microbial composition ...

Degradation of polychlorinated biphenyls in the rhizosphere of rape, Brassica napus L.

Science.gov (United States)

Javorská, Hana; Tlustos, Pavel; Kaliszová, Regina

2009-06-01

The objective of this study was to investigate the rhizosphere effect of rape plants on polychlorinated biphenyls (PCB) dissipation in soils spiked with seven indicator congeners. Depletion of PCB in the rhizosphere was significantly higher in the soil with lower organic matter content. While in the Chernozem soil, 87% of PCB related to bulk soil were found in the 1st mm from roots, only 62%-69% were found in the Fluvisol soil with no significant influence of increased initial PCB concentration. Further from the roots, the concentration of lower chlorinated congeners decreased, which indicates their greater biodegradation in comparison with more chlorinated ones.

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

Science.gov (United States)

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.

Comparative plant uptake and microbial degradation of trichloroethylene in the rhizospheres of five plant species-- implications for bioremediation of contaminated surface soils

Energy Technology Data Exchange (ETDEWEB)

Anderson, T. A. [Tennessee Univ., Knoxville, TN (United States); Walton, B. T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

1992-01-01

The objective of this study was to collect data that would provide a foundation for the concept of using vegetation to enhance in situ bioremediation of contaminated surface soils. Soil and vegetation (Lespedeza cuneata, Paspalum notatum, Pinus taeda, and Solidago sp.) samples from the Miscellaneous Chemicals Basin (MCB) at the Savannah River Site were used in tests to identify critical plant and microbiological variables affecting the fate of trichloroethylene (TCE) in the root zone. Microbiological assays including phospholipid acid analyses, and 14C-acetate incorporation were conducted to elucidate differences in rhizosphere and nonvegetated soil microbial communities from the MCB. The microbial activity, biomass, and degradation of TCE in rhizosphere soils were significantly greater than corresponding nonvegetated soils. Vegetation had a positive effect on microbial degradation of 14C-TCE in whole-plant experiments. Soils from the MCB containing Lespedeza cuneata, Pinus taeda, and Glycine max mineralized greater than 25% of the 14C- TCE added compared with less than 20% in nonvegetated soils. Collectively, these results provide evidence for the positive role of vegetation in enhancing biodegradation.

Comparative plant uptake and microbial degradation of trichloroethylene in the rhizospheres of five plant species-- implications for bioremediation of contaminated surface soils

Energy Technology Data Exchange (ETDEWEB)

Anderson, T.A. (Tennessee Univ., Knoxville, TN (United States)); Walton, B.T. (Oak Ridge National Lab., TN (United States))

1992-01-01

The objective of this study was to collect data that would provide a foundation for the concept of using vegetation to enhance in situ bioremediation of contaminated surface soils. Soil and vegetation (Lespedeza cuneata, Paspalum notatum, Pinus taeda, and Solidago sp.) samples from the Miscellaneous Chemicals Basin (MCB) at the Savannah River Site were used in tests to identify critical plant and microbiological variables affecting the fate of trichloroethylene (TCE) in the root zone. Microbiological assays including phospholipid acid analyses, and {sup 14}C-acetate incorporation were conducted to elucidate differences in rhizosphere and nonvegetated soil microbial communities from the MCB. The microbial activity, biomass, and degradation of TCE in rhizosphere soils were significantly greater than corresponding nonvegetated soils. Vegetation had a positive effect on microbial degradation of {sup 14}C-TCE in whole-plant experiments. Soils from the MCB containing Lespedeza cuneata, Pinus taeda, and Glycine max mineralized greater than 25% of the {sup 14}C- TCE added compared with less than 20% in nonvegetated soils. Collectively, these results provide evidence for the positive role of vegetation in enhancing biodegradation.

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

Science.gov (United States)

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 (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.

Antifungal activity of bacterial strains from the rhizosphere of ...

African Journals Online (AJOL)

This study evaluated the antifungal action of biomolecules produced from the secondary metabolism of bacterial strains found in the rhizosphere of semi arid plants against human pathogenic Candida albicans. Crude extracts were obtained using ethyl acetate as an organic solvent and the bioactivity was assessed with a ...

Effects of different rhizosphere ventilation treatment on water and ...

African Journals Online (AJOL)

The objective of this study was to explore the effects of different rhizosphere ventilation treatment on water and nutrients absorption of maize. The pot experiment was conducted using three methods: no ventilation, two day ventilation and four day ventilation, under conditions of the different levels of irrigation methods.

Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing.

Science.gov (United States)

Uhlik, Ondrej; Jecna, Katerina; Mackova, Martina; Vlcek, Cestmir; Hroudova, Miluse; Demnerova, Katerina; Paces, Vaclav; Macek, Tomas

2009-10-01

DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [(13)C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase alpha subunits (BphA) from bacteria that incorporated [(13)C]into DNA in 3-day incubations of the soils with [(13)C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems

Directory of Open Access Journals (Sweden)

Juan Ling

2018-01-01

Full Text Available Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA and bacteria (AOB, yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR assays, targeting the ammonia monooxygenase-subunit (amoA genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root at the DNA level (P < 0.05. Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle

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

Science.gov (United States)

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

Can inoculation with living soil standardize microbial communities in soilless potting substrates?

Czech Academy of Sciences Publication Activity Database

Bukovská, P.; Püschel, David; Hršelová, H.; Jansa, J.; Gryndler, M.

2016-01-01

Roč. 108, 01 DEC (2016), s. 278-287 ISSN 0929-1393 R&D Projects: GA MŠk 1M0571 Institutional support: RVO:67985939 Keywords : microbial community profiling * compost * rhizosphere Subject RIV: EF - Botanics Impact factor: 2.786, year: 2016

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

Science.gov (United States)

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.

Research on Community Structure in Bus Transport Networks

International Nuclear Information System (INIS)

Yang Xuhua; Wang Bo; Sun Youxian

2009-01-01

We abstract the bus transport networks (BTNs) to two kinds of complex networks with space L and space P methods respectively. Using improved community detecting algorithm (PKM agglomerative algorithm), we analyze the community property of two kinds of BTNs graphs. The results show that the BTNs graph described with space L method have obvious community property, but the other kind of BTNs graph described with space P method have not. The reason is that the BTNs graph described with space P method have the intense overlapping community property and general community division algorithms can not identify this kind of community structure. To overcome this problem, we propose a novel community structure called N-depth community and present a corresponding community detecting algorithm, which can detect overlapping community. Applying the novel community structure and detecting algorithm to a BTN evolution model described with space P, whose network property agrees well with real BTNs', we get obvious community property. (general)

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

Science.gov (United States)

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.

Effects of Azospirillum brasilense with genetically modified auxin biosynthesis gene ipdC upon the diversity of the indigenous microbiota of the wheat rhizosphere.

Science.gov (United States)

Baudoin, Ezékiel; Lerner, Anat; Mirza, M Sajjad; El Zemrany, Hamdy; Prigent-Combaret, Claire; Jurkevich, Edouard; Spaepen, Stijn; Vanderleyden, Jos; Nazaret, Sylvie; Okon, Yaacov; Moënne-Loccoz, Yvan