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  • Bacteria
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  • 1
    In: PLoS ONE, 2014, Vol.9(8)
    Description: 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 the bottom rot disease severity.
    Keywords: Research Article ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 2
    In: PLoS ONE, 2015, Vol.10(7)
    Description: Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils (model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: 2012, Vol.7(10), p.e44685
    Description: The western corn rootworm (WCR) is one of the economically most important pests of maize. A better understanding of microbial communities associated with guts and eggs of the WCR is required in order to develop new pest control strategies, and to assess the potential role of the WCR in the dissemination of microorganisms, e.g., mycotoxin-producing fungi. ; Total community (TC) DNA was extracted from maize rhizosphere, WCR eggs, and guts of larvae feeding on maize roots grown in three different soil types. Denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene and ITS fragments, PCR-amplified from TC DNA, were used to investigate the fungal and bacterial communities, respectively. Microorganisms in the WCR gut were not influenced by the soil type. Dominant fungal populations in the gut were affiliated to spp., while was the most abundant bacterial genus. Identical ribosomal sequences from gut and egg samples confirmed a transovarial transmission of sp. Betaproteobacterial DGGE indicated a stable association of sp. with the WCR gut. Dominant egg-associated microorganisms were the bacterium sp. and the fungus ; The soil type-independent composition of the microbial communities in the WCR gut and the dominance of only a few microbial populations suggested either a highly selective environment in the gut lumen or a high abundance of intracellular microorganisms in the gut epithelium. The dominance of species in the guts indicated WCR larvae as vectors of mycotoxin-producing fungi. The stable association of sp. with WCR gut systems and the absence of corresponding sequences in WCR eggs suggested that this bacterium was postnatally acquired from the environment. The present study provided new insights into the microbial communities associated with larval guts and eggs of the WCR. However, their biological role remains to be explored.
    Keywords: Research Article ; Agriculture ; Biology ; Plant Biology ; Microbiology
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Applied and environmental microbiology, February 2013, Vol.79(4), pp.1410-3
    Description: To study the role of broad-host-range IncP-1 plasmids in bacterial adaptability to irregular environmental challenges, a quantitative real-time PCR assay was developed that specifically detects the korB gene, which is conserved in all IncP-1 plasmids, in environmental samples. IncP-1 plasmid dynamics in a biopurification system for pesticide wastes were analyzed.
    Keywords: Environmental Microbiology ; Bacteroidetes -- Genetics ; Plasmids -- Analysis
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 5
    Language: English
    In: PLoS ONE, 2011, Vol.6(3), p.e17555
    Description: Mercury-polluted environments are often contaminated with other heavy metals. Therefore, bacteria with resistance to several heavy metals may be useful for bioremediation. Cupriavidus metallidurans CH34 is a model heavy metal-resistant bacterium, but possesses a low resistance to mercury compounds. ; To improve inorganic and organic mercury resistance of strain CH34, the IncP-1β plasmid pTP6 that provides novel , genes and additional other genes was introduced into the bacterium by biparental mating. The transconjugant strain MSR33 was genetically and biochemically characterized. Strain MSR33 maintained stably the plasmid pTP6 over 70 generations under non-selective conditions. The organomercurial lyase protein MerB and the mercuric reductase MerA of strain MSR33 were synthesized in presence of Hg. The minimum inhibitory concentrations (mM) for strain MSR33 were: Hg, 0.12 and CHHg, 0.08. The addition of Hg (0.04 mM) at exponential phase had not an effect on the growth rate of strain MSR33. In contrast, after Hg addition at exponential phase the parental strain CH34 showed an immediate cessation of cell growth. During exposure to Hg no effects in the morphology of MSR33 cells were observed, whereas CH34 cells exposed to Hg showed a fuzzy outer membrane. Bioremediation with strain MSR33 of two mercury-contaminated aqueous solutions was evaluated. Hg (0.10 and 0.15 mM) was completely volatilized by strain MSR33 from the polluted waters in presence of thioglycolate (5 mM) after 2 h. ; A broad-spectrum mercury-resistant strain MSR33 was generated by incorporation of plasmid pTP6 that was directly isolated from the environment into CH34. Strain MSR33 is capable to remove mercury from polluted waters. This is the first study to use an IncP-1β plasmid directly isolated from the environment, to generate a novel and stable bacterial strain useful for mercury bioremediation.
    Keywords: Research Article ; Biology ; Microbiology ; Biotechnology
    E-ISSN: 1932-6203
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  • 6
    In: PLoS ONE, 2018, Vol.13(10)
    Description: Apple replant disease (ARD) is the phenomenon of soil decline occurring after repeated planting of apple trees at the same site. This study aimed to elucidate whether ARD is systemic, i.e. whether the contact of parts of the root system with ARD soil causes the whole plant to show poor shoot and root growth. A split-root experiment was conducted with seedlings of ‘M26’, offering the same plant for its root system the choice between the substrates ARD soil (+ARD), γ-sterilized ARD soil (-ARD) or soil from a grass parcel (Control) with the following combinations: +ARD/+ARD, -ARD/-ARD; +ARD/-ARD; +ARD/Control. Root growth was analysed throughout the 34-day growing period. Samples from bulk, rhizosphere and rhizoplane soil were collected separately for each compartment, and analysed by fingerprints of 16S rRNA gene or ITS fragments amplified from total community (TC) DNA. The response of the plant to +ARD was not systemic as root growth in -ARD compartment was always superior to root growth in +ARD soil. Crosswise 15 N-labelling of the N-fertilizer applied to the split-root compartments showed that nitrate-N uptake efficiency was higher for roots in -ARD soil compared to those in +ARD. Bacterial and fungal community composition in the rhizoplane and rhizosphere of the same plants differed significantly between the compartments containing +ARD/-ARD or +ARD/Control. The strongest differences between the bacterial fingerprints were observed in the rhizoplane and rhizosphere. Bacterial genera with increased abundance in response to ARD were mainly Streptomyces but also Sphingobium , Novosphingobium , Rhizobium , Lysobacter and Variovorax . The strongest differences between the fungal fingerprints were observed in bulk soil. Our data showed that the response of the apple plant to ARD soil is local and not systemic.
    Keywords: Research Article ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Medicine And Health Sciences ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 7
    Language: English
    In: Applied Microbiology and Biotechnology, 2016, Vol.100(21), pp.9343-9353
    Description: Pig manures are frequently used as fertilizer or co-substrate in biogas plants (BGPs) and typically contain antibiotic residues (ARs), as well as bacteria carrying resistance genes (RGs) and mobile genetic elements (MGEs). A survey of manures from eight pig fattening and six pig breeding farms and digestates from eight BGPs in Lower Saxony, Germany was conducted to evaluate the link between antibiotic usage and ARs to RGs and MGEs present in organic fertilizers. In total, 11 different antibiotics belonging to six substance classes were applied in the farms investigated. Residue analysis revealed concentrations of tetracycline up to 300 mg kg −1 dry weight (DW) in manures and of doxycycline up to 10.1 mg kg −1 DW in digestates indicating incomplete removal during anaerobic digestion. RGs ( sul1 , sul2 , tet (A), tet (M), tet (X), qacE ∆ 1 ) were detected in total community DNA of all samples by PCR-Southern blot hybridization. Broad-host range plasmids (IncP-1, IncQ, IncN, and IncW) and integron integrase genes ( intI1 , intI2 ) were found in most manure samples with IncN and IncW plasmids being more abundant in manure from pig breeding compared to pig fattening farms. IntI1 , IncQ, and IncW plasmids were also detected in all digestates, while IncP-1, IncN, and LowGC plasmids were detected only sporadically. Our findings strongly reinforce the need for further research to identify mitigation strategies to reduce the level of contamination of organic fertilizers with ARs and transferable RGs that are applied to soil and that might influence the mobile resistome of the plant microbiome.
    Keywords: Antibiotic resistance genes ; Mobile genetic elements ; Antibiotics ; Pig husbandry ; Manures ; Digestates
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 8
    Language: English
    In: Journal of Hazardous Materials, 2010, Vol.184(1), pp.523-532
    Description: Twenty-six different plant species were analyzed regarding their performance in soil contaminated with petroleum oil. Two well-performing species, Italian ryegrass ( var. Taurus), Birdsfoot trefoil ( var. Leo) and the combination of these two plants were selected to study the ecology of plant-associated, culturable alkane-degrading bacteria. Hydrocarbon degrading bacteria were isolated from the rhizosphere, root interior and shoot interior and subjected to the analysis of 16S rRNA gene, the 16S and 23S rRNA intergenic spacer region and alkane hydroxylase genes. Furthermore, we investigated whether alkane hydroxylase genes are plasmid located. Higher numbers of culturable, alkane-degrading bacteria were associated with Italian ryegrass, which were also characterized by a higher diversity, particularly in the plant interior. Only half of the isolated bacteria hosted known alkane hydroxylase genes ( and cytochrome P153-like). Degradation genes were found both on plasmids as well as in the chromosome. In regard to application of plants for rhizodegradation, where support of numerous degrading bacteria is essential for efficient break-down of pollutants, Italian ryegrass seems to be more appropriate than Birdsfoot trefoil.
    Keywords: Alkane Hydroxylase ; 16s Rrna Gene ; Rhizosphere ; Endophytes ; Italian Ryegrass ; Birdsfoot Trefoil ; Engineering ; Law
    ISSN: 0304-3894
    E-ISSN: 1873-3336
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  • 9
    Language: English
    In: PLoS ONE, 2012, Vol.7(5), p.e37288
    Description: Larvae of the Western Corn Rootworm (WCR) feeding on maize roots cause heavy economical losses in the US and in Europe. New or adapted pest management strategies urgently require a better understanding of the multitrophic interaction in the rhizosphere. This study aimed to investigate the effect of WCR root feeding on the microbial communities colonizing the maize rhizosphere. ; In a greenhouse experiment, maize lines KWS13, KWS14, KWS15 and MON88017 were grown in three different soil types in presence and in absence of WCR larvae. Bacterial and fungal community structures were analyzed by denaturing gradient gel electrophoresis (DGGE) of the16S rRNA gene and ITS fragments, PCR amplified from the total rhizosphere community DNA. DGGE bands with increased intensity were excised from the gel, cloned and sequenced in order to identify specific bacteria responding to WCR larval feeding. DGGE fingerprints showed that the soil type and the maize line influenced the fungal and bacterial communities inhabiting the maize rhizosphere. WCR larval feeding affected the rhiyosphere microbial populations in a soil type and maize line dependent manner. DGGE band sequencing revealed an increased abundance of in the rhizosphere of several maize lines in all soil types upon WCR larval feeding. ; The effects of both rhizosphere and WCR larval feeding seemed to be stronger on bacterial communities than on fungi. Bacterial and fungal community shifts in response to larval feeding were most likely due to changes of root exudation patterns. The increased abundance of suggested that phenolic compounds were released upon WCR wounding.
    Keywords: Research Article ; Agriculture ; Biology ; Genetics And Genomics ; Plant Biology ; Biotechnology ; Ecology
    E-ISSN: 1932-6203
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  • 10
    In: Molecular Ecology, March 2014, Vol.23(6), pp.1392-1404
    Description: Salt marsh sediments are sinks for various anthropogenic contaminants, giving rise to significant environmental concern. The process of salt marsh plant survival in such environment is very intriguing and at the same time poorly understood. The plant–microbe interactions may play a key role in the process of environment and detoxification. In this study, a combination of culture‐dependent and culture‐independent molecular approaches [enrichment cultures, polymerase chain reaction (), denaturing gradient gel electrophoresis (), sequencing] were used to investigate the effect of petroleum hydrocarbons () contamination on the structure and function [polycyclic aromatic hydrocarbon () dioxygenase genes] of endophytic bacterial communities of salt marsh plant species ( and ) in the estuarine system Ria de Aveiro (Portugal). Pseudomonads dominated the cultivable fraction of the endophytic communities in the enrichment cultures. In a set of fifty isolates tested, nine were positive for genes encoding for dioxygenases () and four were positive for plasmid carrying genes encoding degradation enzymes (c). Interestingly, these plasmids were only detected in isolates from most severely ‐polluted sites. The results revealed site‐specific effects on endophytic communities, related to the level of contamination in the sediment, and plant‐species‐specific ‘imprints’ in community structure and in genes encoding for dioxygenases. These results suggest a potential ecological role of bacterial plant symbiosis in the process of plant colonization in urban estuarine areas exposed to contamination.
    Keywords: Endophytic ; ‐Degrading Genes ; Polycyclic Aromatic Hydrocarbon ; Salt Marsh Plants
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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