Research Topics
Genomes and Genes | K SmallaSummaryAffiliation: Federal Biological Research Centre for Agriculture and Forestry Country: Germany Publications
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Publications
Exogenous isolation of antibiotic resistance plasmids from piggery manure slurries reveals a high prevalence and diversity of IncQ-like plasmidsK Smalla
Biologische Bundesanstalt für Land und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, D 38104 Braunschweig, Germany
Appl Environ Microbiol 66:4854-62. 2000..These findings suggest that IncQ plasmids play an important role in disseminating antibiotic resistance genes...
Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results?Kornelia Smalla
Biologische Bundesanstalt für Land und Forstwirtschaft BBA, Messeweg 11 12, 38104 Braunschweig, Germany
J Microbiol Methods 69:470-9. 2007....- Horizontal gene transfer between bacteriaHolger Heuer
Federal Biological Research Centre for Agriculture and Forestry BBA, Braunschweig, Germany
Environ Biosafety Res 6:3-13. 2007..In view of the use of GM crops and microbes in agricultural settings, in this mini-review we focus particularly on the presence and role of MGE in soil and plant-associated bacteria and the factors affecting gene transfer... - Screening of rhizosphere and soil bacteria for transformabilityBabette Richter
Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Messeweg 11 12, 38104, Braunschweig, Germany
Environ Biosafety Res 6:91-9. 2007..The various transformation assays performed indicate that the proportion of rhizosphere or bulk soil bacteria which are naturally transformable is negligibly low... - Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory elementKornelia Smalla
Federal Biological Research Centre for Agriculture and Forestry BBA, Messeweg 11 12, 38104 Braunschweig, Germany
Appl Environ Microbiol 72:7253-9. 2006..This transposon carries a rather complex set of mer genes and is inserted between Tra1 and Tra2... - Field releases of genetically modified micro-organismsKornelia Smalla
Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Messeweg 11/12, 38104 Braunschweig, Germany
Environ Biosafety Res 2:65-8. 2003 - Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealedK Smalla
Federal Biological Research Centre for Agriculture and Forestry, D 38104 Braunschweig, D 18051 Rostock, Germany
Appl Environ Microbiol 67:4742-51. 2001..Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands... - The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approachesKornelia Smalla
Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Messeweg 11 12, D 38104 Braunschweig, Germany
FEMS Microbiol Ecol 42:165-75. 2002.... - Short-term effects of amoxicillin on bacterial communities in manured soilChu Thi Thanh Binh
Federal Biological Research Centre for Agriculture and Forestry, Braunschweig, Germany
FEMS Microbiol Ecol 62:290-302. 2007..Molecular fingerprint analysis of 16S rRNA gene fragments amplified from soil DNA revealed significant effects of manure and amoxicillin on the bacterial community of both soils... - Diversity of ndo genes in mangrove sediments exposed to different sources of polycyclic aromatic hydrocarbon pollutionNewton C Marcial Gomes
Federal Biological Research Centre for Agriculture and Forestry BBA, Braunschweig, Germany
Appl Environ Microbiol 73:7392-9. 2007..The long-term impact of PAH contamination, together with the specific environmental conditions at each site, may have affected the abundance and diversity of ndo genes in sediments of urban mangroves... - Specific and sensitive detection of Ralstonia solanacearum in soil on the basis of PCR amplification of fliC fragmentsJ Schonfeld
Institute for Plant Virology, Microbiology, and Biosafety, Federal Biological Research Centre for Agriculture and Forestry, 38104 Braunschweig, Germany
Appl Environ Microbiol 69:7248-56. 2003..The system was applied to survey soils from different geographic origins for the presence of R. solanacearum... 
Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manureChu T T Binh
Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institut, Federal Research Centre for Cultivated Plants JKI, Messeweg 11 12, D 38104 Braunschweig, Germany
Res Microbiol 160:427-33. 2009..In addition, class 1 integrons without gene cassettes were detected in total community DNA of many manures...- Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes by using a novel PCR detection systemGuo Chun Ding
Julius Kühn Institut, Messeweg, D 38104 Braunschweig, Germany
Appl Environ Microbiol 76:4765-71. 2010..In conclusion, sequence analysis of the amplicons obtained confirmed the specificity of the novel primer system and revealed a soil type-dependent response of PAH-RHD(alpha) gene-carrying soil bacteria to phenanthrene spiking... - Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two monthsHolger Heuer
Federal Biological Research Centre for Agriculture and Forestry BBA, Braunschweig, Germany
Environ Microbiol 9:657-66. 2007..The synergistic effects of manure and SDZ were still detectable after 2 months. The results suggest that manure from treated pigs enhances spread of antibiotic resistances in soil bacterial communities... - Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guildsRodrigo Costa
Federal Biological Research Centre for Agriculture and Forestry, Braunschweig, Germany
FEMS Microbiol Ecol 56:236-49. 2006..and Rhizobium sp. were among the dominant ribotypes in the strawberry rhizosphere, while sequences from Arthrobacter sp. corresponded to dominant bands from oilseed rape bacterial fingerprints... - Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analysesRodrigo Costa
Federal Biological Research Centre for Agriculture and Forestry BBA, Messeweg 11 12, D 38104 Braunschweig, Germany
Environ Microbiol 9:2260-73. 2007..Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis... - Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropicsNewton C Marcial Gomes
, , Mikrobiologie und biologische Sicherheit, Messeweg 11-12, 38104 Braunschweig, Germany
Appl Environ Microbiol 69:3758-66. 2003.... - In vitro antagonists of Rhizoctonia solani tested on lettuce: rhizosphere competence, biocontrol efficiency and rhizosphere microbial community responseModupe F Adesina
Julius Kühn Institut Federal Research Centre for Cultivated Plants JKI, D 38104 Braunschweig, Germany
FEMS Microbiol Ecol 69:62-74. 2009..Although the exact mechanism of antagonistic activity and the ecology of RU47 remain to be further explored, our results suggest that RU47 is a promising agent to control bottom rot of lettuce... - Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plantsRodrigo Costa
Federal Biological Research Centre for Agriculture and Forestry (BBA, Messeweg 11/12, D-38104 Braunschweig, Germany
Environ Microbiol 8:2136-49. 2006..This report provides a better understanding of how different factors drive Pseudomonas community structure and diversity in bulk and rhizosphere soils... - Effects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factorsHolger Heuer
Federal Biological Research Centre for Agriculture and Forestry, Institute for Microbiology, Plant Virology and Biosafety, Messeweg 11-12, D-38104 Braunschweig, Germany
Appl Environ Microbiol 68:1325-35. 2002.... - Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae klebGabriele Berg
University of Rostock, Fachbereich Biowissenschaften, Microbiology, D 18051 Rostock, Germany
Appl Environ Microbiol 71:4203-13. 2005..A broad spectrum of new Verticillium antagonists was identified, and the implications of the data for biocontrol applications are discussed... - A new semi-nested PCR protocol to amplify large 18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communitiesMiruna Oros-Sichler
, , Mikrobiologie und biologische Sicherheit, Messeweg 11-12, 38104 Braunschweig, Germany
J Microbiol Methods 65:63-75. 2006..The semi-nested PCR system developed in this study, coupled with DGGE fingerprinting, offers a robust, reliable and sensitive tool for the analysis of soil fungal community structure... - Survival of gfp-tagged antagonistic bacteria in the rhizosphere of tomato plants and their effects on the indigenous bacterial communityMonika Götz
Institute for Plant Virology, Microbiology and Biosafety, Federal Biological Research Centre for Agriculture and Forestry, Braunschweig, Germany
FEMS Microbiol Ecol 56:207-18. 2006..The colonization patterns observed by CLSM provide important information on the sampling strategy required for monitoring inoculant strains in the rhizosphere... - Variation in permissiveness for broad-host-range plasmids among genetically indistinguishable isolates of Dickeya sp. from a small field plotHolger Heuer
Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11 12, Braunschweig, Germany
FEMS Microbiol Ecol 73:190-6. 2010..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... - Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methodsMonika Götz
Institute for Plant Virology, Microbiology and Biosafety, Federal Biological Research Centre for Agriculture and Forestry BBA, Braunschweig, Germany
FEMS Microbiol Ecol 58:404-13. 2006..Differences in the relative abundance of endophytic fungi colonizing the roots of T4-lysozyme producing potatoes and the parental line could be detected by both methods... - The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphereAndreas Tauch
Zentrum für Genomforschung, Universitat Bielefeld, D 33615 Bielefeld, Germany
Microbiology 148:1637-53. 2002..These data add to the growing evidence that plasmids carry advantageous genes with as yet undefined functions in plant-associated communities... - Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertaintyHolger Heuer
Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Braunschweig, Germany
FEMS Microbiol Ecol 65:361-71. 2008..Consequently, mechanisms that make a subpopulation conducive to specific conjugative plasmids may have evolved, which could explain the persistence of even cryptic plasmids that do not encode any traits... - Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmidsChu Thi Thanh Binh
Julius Kühn Institute, Federal Research Centre for Cultivated Crops, Braunschweig, Germany
FEMS Microbiol Ecol 66:25-37. 2008..This study showed that 'field-scale' piggery manure is a reservoir of broad-host range plasmids conferring multiple antibiotic resistance genes... - Exploring the diversity of bacterial communities in sediments of urban mangrove forestsNewton C Marcial Gomes
Julius Kühn Institute for Cultivated Crops, Messeweg, Braunschweig, Germany
FEMS Microbiol Ecol 66:96-109. 2008..Many dominant DGGE ribotypes showed low levels of sequence identity to known sequences, indicating a large untapped bacterial diversity in mangrove ecosystems... - Significance test for comparing complex microbial community fingerprints using pairwise similarity measuresSiegfried Kropf
Institute for Biometry and Medical Informatics, Otto von Guericke University, Leipziger Str 44, Magdeburg 39120, Germany
J Microbiol Methods 57:187-95. 2004..An example is given for the comparison of bacterial soil communities, testing the effect of different crop plants. Each community was represented by amplified ribosomal gene fragments separated in a denaturing gradient gel... - Community structure of actively growing bacterial populations in plant pathogen suppressive soilKarin Hjort
Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE 750 07, Uppsala, Sweden
Microb Ecol 53:399-413. 2007..These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil... - The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs depending on plant species and siteGabriele Berg
Institute for Life Sciences, University of Rostock, Microbiology, Rostock, Germany
FEMS Microbiol Ecol 56:250-61. 2006..Antagonists of the genus Serratia were preferentially isolated from oilseed rape rhizosphere, with the exception of one site. For isolates of Pseudomonas and Serratia, plant-specific and site-specific genotypes were found... - The rhizosphere: 'soil compartment influenced by the root'Kornelia Smalla
FEMS Microbiol Ecol 56:165. 2006 - Molecular classification of IncP-9 naphthalene degradation plasmidsTatyana Yu Izmalkova
G K Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
Plasmid 56:1-10. 2006..Discovery of a large group of plasmid with unique nahR suggested that the regulatory loop may also represent a variable part of the pathway for catabolism of naphthalene in fluorescent Pseudomonas spp... - Diversity of IncP-9 plasmids of PseudomonasYanina R Sevastsyanovich
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
Microbiology 154:2929-41. 2008.... - Comparison of independent samples of high-dimensional data by pairwise distance measuresSiegfried Kropf
Institute of Biometry and Medical Informatics, Otto von Guericke University, Magdeburg, Germany
Biom J 49:230-41. 2007..As the number of possible permutations is small in very small samples, this might restrict the use of the test. Therefore, we propose an exact parametric small sample version of the test using randomly rotated samples... - Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial communityNewton C M Gomes
Federal Biological Research Centre for Agriculture and Forestry (BBA, Braunschweig, Germany
FEMS Microbiol Ecol 54:21-33. 2005..Although the inoculant strain KT2442 (pNF142) showed good survival and expression of genes involved in naphthalene degradation, this study suggests that KT2442 (pNF142) suppressed the enrichment of indigenous naphthalene degraders... - PCR detection of oxytetracycline resistance genes otr(A) and otr(B) in tetracycline-resistant streptomycete isolates from diverse habitatsTheodora L Nikolakopoulou
Department of Botany, Microbiology Group, National and Kapodistrian University of Athens, Faculty of Biology, Greece
Curr Microbiol 51:211-6. 2005..Our results indicated that the occurrence of otr(A) and otr(B) genes in natural environments was limited and that otr(B), in comparison to otr(A), seemed to be more common... - Microbial community networksKornelia Smalla
FEMS Microbiol Ecol 66:1-2. 2008 - Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plantsGabriele Berg
Department of Microbiology, Institute for Molecular Physiology and Biotechnology, University of Rostock, D 18055 Rostock, Germany
Appl Environ Microbiol 68:3328-38. 2002..Pantoea agglomerans) were mainly isolated from the rhizosphere of oilseed rape. For P. putida A and B plant-specific genotypes were observed, suggesting that these bacteria were specifically enriched in each rhizosphere... - Repeat domain diversity of avrBs3-like genes in Ralstonia solanacearum strains and association with host preferences in the fieldHolger Heuer
Department of Plant Pathology, Nanjing Agricultural University, Weigang No 1, Nanjing, China
Appl Environ Microbiol 73:4379-84. 2007..A statistically significant association between the originating plant species and internal repeats of the gene was found. Sequences of repeats and variation between nearly clonal strains revealed evidence of frequent recombination...