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Berlin Brandenburg

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  • 1
    Language: English
    In: Applied and environmental microbiology, May 2014, Vol.80(9), pp.2679-86
    Description: Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity.
    Keywords: Bacteria -- Isolation & Purification ; Fungi -- Isolation & Purification ; Lycopersicon Esculentum -- Parasitology ; Plant Diseases -- Parasitology ; Tylenchoidea -- Microbiology
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 2
    In: PLoS ONE, 2014, Vol.9(2)
    Description: The potential of bacterial antagonists of fungal pathogens to control the root-knot nematode Meloidogyne incognita was investigated under greenhouse conditions. Treatment of tomato seeds with several strains significantly reduced the numbers of galls and egg masses compared with the untreated control. Best performed Bacillus subtilis isolates Sb4-23, Mc5-Re2, and Mc2-Re2, which were further studied for their mode of action with regard to direct effects by bacterial metabolites or repellents, and plant mediated effects. Drenching of soil with culture supernatants significantly reduced the number of egg masses produced by M. incognita on tomato by up to 62% compared to the control without culture supernatant. Repellence of juveniles by the antagonists was shown in a linked twin-pot set-up, where a majority of juveniles penetrated roots on the side without inoculated antagonists. All tested biocontrol strains induced systemic resistance against M. incognita in tomato, as revealed in a split-root system where the bacteria and the nematodes were inoculated at spatially separated roots of the same plant. This reduced the production of egg masses by up to 51%, while inoculation of bacteria and nematodes in the same pot had only a minor additive effect on suppression of M. incognita compared to induced systemic resistance alone. Therefore, the plant mediated effect was the major reason for antagonism rather than direct mechanisms. In conclusion, the bacteria known for their antagonistic potential against fungal pathogens also suppressed M. incognita . Such “multi-purpose” bacteria might provide new options for control strategies, especially with respect to nematode-fungus disease complexes that cause synergistic yield losses.
    Keywords: Research Article ; Agriculture ; Biology
    E-ISSN: 1932-6203
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  • 3
    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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  • 4
    Language: English
    In: New Phytologist, August, 2013, Vol.199(3), p.773(14)
    Description: Byline: Orlando Lange, Tom Schreiber, Niklas Schandry, Jara Radeck, Karl Heinz Braun, Julia Koszinowski, Holger Heuer, Annett Strau[sz], Thomas Lahaye Keywords: AvrBs3 (avirulence protein triggering Bs3 resistance); Brg11(hrpB-regulated 11); designer transcription activator-like effector (TALE); GMI1000; Ralstonia solanacearum ; Ralstonia transcription activator-like effector (TALE)-like (RTL); repeat variable diresidue (RVD); transcription activator-like (TAL) effectors Summary Ralstonia solanacearum is a devastating bacterial phytopathogen with a broad host range. Ralstonia solanacearum injected effector proteins (Rips) are key to the successful invasion of host plants. We have characterized Brg11(hrpB-regulated 11), the first identified member of a class of Rips with high sequence similarity to the transcription activator-like (TAL) effectors of Xanthomonas spp., collectively termed RipTALs. Fluorescence microscopy of in planta expressed RipTALs showed nuclear localization. Domain swaps between Brg11 and Xanthomonas TAL effector (TALE) AvrBs3 (avirulence protein triggering Bs3 resistance) showed the functional interchangeability of DNA-binding and transcriptional activation domains. PCR was used to determine the sequence of brg11 homologs from strains infecting phylogenetically diverse host plants. Brg11 localizes to the nucleus and activates promoters containing a matching effector-binding element (EBE). Brg11 and homologs preferentially activate promoters containing EBEs with a 5a[sup.2] terminal guanine, contrasting with the TALE preference for a 5a[sup.2] thymine. Brg11 and other RipTALs probably promote disease through the transcriptional activation of host genes. Brg11 and the majority of homologs identified in this study were shown to activate similar or identical target sequences, in contrast to TALEs, which generally show highly diverse target preferences. This information provides new options for the engineering of plants resistant to R. solanacearum. Author Affiliation: Supporting information: Additional Supporting Information may be found in the online version of this article Please note: Wiley-Blackwell are not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office.
    Keywords: Purines ; Plant Genetics ; Plants (Organisms) ; Proteins ; Bacterial Infections ; Transcription (Genetics) ; Genetic Research ; Bacterial Genetics ; Fluorescence ; Genes ; Dna
    ISSN: 0028-646X
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  • 5
    Language: English
    In: Biometrical Journal, Jan, 2012, Vol.54(1), p.94(14)
    Description: Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia , Shinella , Stenotrophomonas , Clostridium , Peptostreptococcus , Leifsonia , Gemmatimonas , were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter , Hydrogenophaga , and Adhaeribacter decreased in response to the repeated application of manure and SDZ.
    Keywords: Medical Informatics -- Analysis ; Potatoes -- Analysis
    ISSN: 0323-3847
    ISSN: 19326203
    E-ISSN: 19326203
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  • 6
    In: FEMS Microbiology Ecology, 2010, Vol. 73(1), pp.190-196
    Description: Phytopathogenic populations need genetic flexibility to adapt to continually improving plant defences. The gene pool transferred by broad-host-range plasmids provides genetic variation for the population. However, a population has to balance this benefit with the risk of acquiring deleterious foreign DNA. This could be achieved by modulating the ratio of individuals with high or low permissiveness to broad-host-range plasmids. We investigated whether plasmid uptake varied among genetically indistinguishable isolates of Dickeya sp. from a 400 m 2 field plot. The transfer frequencies of broad-host-range IncP-1 plasmids from Escherichia coli to Dickeya differed significantly among isolates. The transfer frequencies for plasmids pTH10 and pB10 of the divergent α- and β-subgroups of IncP-1, respectively, correlated well. Strains that differed in permissiveness for these plasmids by orders of magnitude were not distinguishable by other phenotypic traits analysed, by genomic fingerprints or hrpN gene sequences. Such strains were isolated in close vicinity and from different plots of the field, indicating a reasonably fast genetic mechanism of switching between low and high permissiveness.
    Keywords: Bacterial Population Heterogeneity ; Plasmid Ecology ; Broad - Host - Range Plasmids ; Evolvability ; Adaptability ; 〈Kwd〉〈Italic〉Erwinia Chrysanthemi〈/Italic〉〈/Kwd〉
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 7
    Language: English
    In: PLoS ONE, 01 January 2013, Vol.8(3), p.e59497
    Description: Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 8
    Language: German
    In: Julius-Kühn-Archiv, 01 January 2013, Issue 436, pp.115-122
    Description: Soil microbes are of enormous importance for functioning nutrient cycles as well as for plant health. The development and application of nucleic acid based techniques provided new insights into the diversity of bulk and rhizosphere soil microbes. The microbial diversity in soils was shown by means of cultivation-independent methods to be influenced by various biotic and abiotic factors. Sequence based analysis of 16S rRNA genes and ITS fragments amplified from total DNA extracted directly from soil allows to determine the taxonomic affiliation (phylum, class, order, genera and species) of those taxa influenced in their relative abundance by the plant species or genotype, the site, or changes in agricultural management. The diversification within a species and the adaptation of bacterial populations to changing environmental conditions is often fostered by mobile genetic elements. Pathogenicity determinants, genes responsible for the bacterial interaction with its host plant or antibiotic and heavy metal resistance genes are often localized on plasmids. This review summarizes research on microbial diversity performed over more than twenty years at the BBA and now in the JKI in Braunschweig.
    Keywords: Mikrobielle Diversität ; Bakterien ; Pilze ; DNA-Extraktion ; Kultivierbarkeit ; Genetische Flexibilität ; Gentransfer ; Mobile Genetische Elemente ; Microbial Diversity ; Bacteria ; Fungi ; DNA Extraction ; Culturability ; Genetic Flexibility ; Gene Transfer ; Mobile Genetic Elements ; Agriculture
    ISSN: 1868-9892
    ISSN: 2199921X
    Source: Directory of Open Access Journals (DOAJ)
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  • 9
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(5), p.e0177145
    Description: Endoparasitic root-knot (Meloidogyne spp.) and lesion (Pratylenchus spp.) nematodes cause considerable damage in agriculture. Before they invade roots to complete their life cycle, soil microbes can attach to their cuticle or surface coat and antagonize the nematode directly or by induction of host plant defenses. We investigated whether the nematode-associated microbiome in soil differs between infective stages of Meloidogyne incognita and Pratylenchus penetrans, and whether it is affected by variation in the composition of microbial communities among soils. Nematodes were incubated in suspensions of five organically and two integrated horticultural production soils, recovered by sieving and analyzed for attached bacteria and fungi after washing off loosely adhering microbes. Significant effects of the soil type and nematode species on nematode-associated fungi and bacteria were revealed as analyzed by community profiling using denaturing gradient gel electrophoresis. Attached microbes represented a small specific subset of the soil microbiome. Two organic soils had very similar bacterial and fungal community profiles, but one of them was strongly suppressive towards root-knot nematodes. They were selected for deep amplicon sequencing of bacterial 16S rRNA genes and fungal ITS. Significant differences among the microbiomes associated with the two species in both soils suggested specific surface epitopes. Among the 28 detected bacterial classes, Betaproteobacteria, Bacilli and Actinobacteria were the most abundant. The most frequently detected fungal genera were Malassezia, Aspergillus and Cladosporium. Attached microbiomes did not statistically differ between these two soils. However, Malassezia globosa and four fungal species of the family Plectosphaerellaceae, and the bacterium Neorhizobium galegae were strongly enriched on M. incognita in the suppressive soil. In conclusion, the highly specific attachment of microbes to infective stages of phytonematodes in soil suggested an ecological role of this association and might be involved in soil suppressiveness towards them.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 10
    Language: English
    In: Applied and environmental microbiology, December 2012, Vol.78(23), pp.8492-7
    Description: Leaf lesions of Mandevilla sanderi were shown to be caused by Pseudomonas savastanoi. While BOX fingerprints were similar for P. savastanoi isolates from different host plants, plasmid restriction patterns and sequencing of plasmid-located pathogenicity determinants revealed that Mandevilla isolates contained similar plasmids distinct from those of other isolates. A repA-based detection method was established.
    Keywords: Apocynaceae -- Microbiology ; Plant Diseases -- Microbiology ; Pseudomonas -- Isolation & Purification
    ISSN: 00992240
    E-ISSN: 1098-5336
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