André Lipski

University of Bonn, Bonn, North Rhine-Westphalia, Germany

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Publications (57)174.52 Total impact

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    ABSTRACT: Microbial diversity of 3 raw milk samples after 72 h of storage at 4°C in a bulk tank was analyzed by culture-dependent and -independent methods. The culture-dependent approach was based on the isolation of bacteria on complex and selective media, chemotaxonomic differentiation of isolates, and subsequent identification by 16S rRNA gene sequencing. The culture-independent approach included the treatment of raw milk with the dye propidium monoazide before direct DNA extraction by mechanic and enzymatic cell lysis approaches, and cloning and sequencing of the 16S rRNA genes. The selective detection of viable bacteria improved the comparability between bacterial compositions of raw milk based on culture-dependent and -independent methods, which was the major objective of this study. Several bacterial species of the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were detected by the culture-dependent method, whereas mainly bacteria of the phylum Proteobacteria as well as low proportions of the phyla Bacteroidetes and Actinobacteria were detected by the culture-independent method. This led to the conclusion that the phylum Firmicutes was strongly discriminated by the culture-independent approach. Generally, species richness detected by the culture-dependent method was higher than that detected by the culture-independent method for all samples. However, few taxa could be detected solely by the direct DNA-based method. In conclusion, the combination of culture-dependent and -independent methods led to the detection of the highest bacterial diversity for the raw milk samples analyzed. It was shown that DNA extraction from raw milk as the essential step in culture-independent methods causes the discrimination of taxa by incomplete cell lysis. Treatment of raw milk with the viability dye propidium monoazide was optimized for the application in raw milk without former removal of milk ingredients and proved to be a suitable tool to ensure comparability of bacterial diversity depicted by both methods.
    Journal of dairy science. 09/2014;
  • Julia Derichs, Peter Kämpfer, André Lipski
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    ABSTRACT: A Gram-negative, aerobic, rod-shaped, non-motile, non-spore forming bacterial strain, designated J22T, was isolated from a fresh pasta filled with porkmeat (tortellini) that was stored at 6°C. Based on the 16S rRNA gene sequence analysis strain J22T falls within the radiation of the Pedobacter species. On the basis of 16S rRNA gene sequence similarities, the phylogenetically closest species are Pedobacter panaciterrae LMG 23400T (98.7%), Pedobacter africanus DSM 12126T (98.5%), and Pedobacter heparinus DSM 2366T (98.3%). The only isoprenoid quinone of strain J22T was menaquinone 7 (MK-7). The major fatty acids were iso-C15:0 (34.8%), C16:1 cis9 (24.9%), C16:0 (7.3%), C14:0 (4.8%) and iso-C17:0 3-OH (4.4%). These chemotaxonomic characteristics supported the assignment of the isolate to the genus Pedobacter. DNA-DNA hybridization experiments showed that the DNA-DNA similarity between strain J22T and its phylogenetic closest neighbor Pedobacter panaciterrae LMG 23400T was less than 36%. This indicated that the isolate was distinct from this species. Biochemical tests allowed phenotypic differentiation of strain J22T from the next related Pedobacter species. As a consequence, strain J22T should be classified as a representative of a novel species in the genus Pedobacter, for which the name Pedobacter nutrimenti sp. nov. is proposed. The type strain is J22T (= DSM 27372T = CCUG 64422T).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 01/2014; · 2.11 Impact Factor
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    ABSTRACT: Metabolically-active autotrophic nitrite oxidizers from activated sludge were labeled with (13)C-bicarbonate under exposure to different temperatures and nitrite concentrations. The labeled samples were characterized by FAME-SIP (fatty acid methyl ester-stable isotope probing). The compound cis-11-palmitoleic acid, which is the major lipid of the most abundant nitrite oxidizer in activated sludge, Candidatus Nitrospira defluvii, showed (13)C-incorporation in all samples exposed to 3mM nitrite. Subsequently, the lipid cis-7-palmitoleic acid was labeled, and it indicated the activity of a nitrite oxidizer that was different from the known Nitrospira taxa in activated sludge. The highest incorporation of cis-7-palmitoleic acid label was found after incubation with a nitrite concentration of 0.3mM at 17 and 22°C. While activity of Nitrobacter populations could not be detected by the FAME-SIP approach, an unknown nitrite oxidizer with the major lipid cis-9 isomer of palmitoleic acid exhibited (13)C-incorporation at 28°C with 30mM nitrite. These results indicated flexibility of nitrite-oxidizing guilds in a complex community responding to different conditions. Labeled lipids so far not described for activated sludge-associated nitrifiers indicated the presence of unknown nitrite oxidizers in this habitat. The FAME-SIP-based information can be used to define appropriate conditions for the enrichment of nitrite-oxidizing guilds from complex samples.
    Systematic and Applied Microbiology 08/2013; · 3.29 Impact Factor
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    ABSTRACT: Two groups of Gram-positive, aerobic bacterial strains were isolated from cow raw milk, from a milking machine and from bulk tank milk. Based on their 16S rRNA gene sequences these isolates formed two distinct groups within the genus Corynebacterium. The sequence similarities of the isolates to the type strains of the genus Corynebacterium were below 98.4%. The presence of menaquinones MK-8(H2) and MK-9(H2), the predominant fatty acid 18:1 cis9, a polar lipid pattern with several phospholipids but without aminolipids was in accord with the characteristics of this genus. The results of DNA-DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from all known Corynebacterium species. Therefore, the isolates were assigned to two new species of this genus for which the names Corynebacterium frankenforstense sp. nov (type strain ST18 T = DSM 45800T = CCUG 63371T), and Corynebacterium lactis sp. nov. (type strain RW2-5 T = DSM 45799T = CCUG 63372T) are proposed, respectively.
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 08/2013; · 2.11 Impact Factor
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    ABSTRACT: A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultative anaerobic bacterium PB1T was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1T has catalase and low urease activity and hydrolyses gelatine and starch. Strain PB1T is able to grow between -5°C and 30°C with an optimum growth at 14-20°C. Glycerol, D-/L-arabinose, D-xylose, D-galactose, D-fructose, D-lyxose, D-fucose and potassium gluconate are used as sole carbon sources. The major quinone is ubiquinone Q-8. The major fatty acids (>10 %) for PB1T are C16:0 (19.1 %), C16:1ω7cis (44.6 %) and C18:1ω7cis (16.2 %). The major polyamines are putrescine (54.9 μmol g-1 dry weight) and 2-hydroxy-putrescine (18.5 μmol g-1 dry weight). DNA base composition is 62.5 mol% G+C. Strain PB1T is phylogenetically related to species of the genus Herbaspirillum, with highest 16S rRNA gene sequence similarities to Herbaspirillum canariense (97.3%), Herbaspirillum aurantiacum (97.2 %), Herbaspirillum soli (97.2 %) and Herbaspirillum frisingense (97.0 %). The DNA-DNA relatedness values were below 30 % between PB1T and the type strains of H. canariense, H. aurantiacum and H. soli. The different geographical origin of strain PB1T and its next relatives resulted in a different phenotypic and genotypic specification, whereby strain PBT represents a novel species in the genus Herbaspirillum, for which the name Herbaspirillum psychrotolerans is proposed. The type strain is PB1T (DSM 26001T = LMG 27282T).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 03/2013; · 2.11 Impact Factor
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    ABSTRACT: In the scope of diversity studies in glacier forefields on the Larsemann Hills, East Antarctica, a novel psychrotolerant, non-motile Gram-negative, shiny yellow, rod-shaped, aerobic bacterium PB4T was isolated from a soil sample. Strain PB4T produces indole from tryptophan and hydrolyses casein. It grows between 0°C and 25°C with an optimum growth temperature at 20°C. A wide range of substrates are used as sole carbon source and acid is produced from from esculin ferric citrate, D-cellobiose, D-maltose, D-lactose, D-saccharose, D-trehalose, D-melizitose, glycogen, amidon (starch) and gentibiose and weak from D-glucose, amygdalin, salicin and D-turanose. The major menaquinone is MK-6. Identified major fatty acids (>10%) are iso-C15:0 (13.0%) and iso-2OH-C15:0 (51.2%). G+C content is 33.7 mol%. For strain PB4T, highest 16S rRNA gene sequence similarity was found to the type strains of Chryseobacterium humi (97.0%) and Chryseobacterium marinum (96.5%). Considering phenotypic and genotypic characterisation, strain PB4T represents a novel species in the genus Chryseobacterium (Flavobacteriaceae), for which the name Chryseobacterium frigidisoli is proposed. The type strain is PB4T (LMG 27025).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 01/2013; · 2.11 Impact Factor
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    ABSTRACT: Lithoautotrophic nitrite-oxidizing bacterial populations from moving-bed biofilters of brackish recirculation aquaculture systems (RAS; shrimp and barramundi) were tested for their metabolic activity and phylogenetic diversity. Samples from the biofilters were labeled with (13)C-bicarbonate and supplemented with nitrite at concentrations of 0.3, 3 and 10 mM, and incubated at 17 and 28°C, respectively. The biofilm material was analyzed by fatty acid methyl ester - stable isotope probing (FAME-SIP). High portions of up to 45% of Nitrospira-related labeled lipid markers were found confirming that Nitrospira is the major autotrophic nitrite oxidizer in these brackish systems with high nitrogen loads. Other nitrite-oxidizing bacteria such as Nitrobacter or Nitrotoga were functionally not relevant in the investigated biofilters. Nitrospira-related 16S rRNA gene sequences were obtained from the samples with 10 mM nitrite and analyzed by a cloning approach. Sequence studies revealed four different phylogenetic clusters within the marine sublineage IV of Nitrospira, though most sequences clustered with the type strain of Nitrospira marina and with a strain isolated from a marine RAS. Three lipids dominated the whole fatty acid profiles of nitrite-oxidizing marine and brackish enrichments of Nitrospira sublineage IV organisms. The membranes included two marker lipids (16∶1 cis7 and 16∶1 cis11) combined with the non-specific acid 16∶0 as major compounds and confirmed these marker lipids as characteristic for sublineage IV species. The predominant labeling of these characteristic fatty acids and the phylogenetic sequence analyses of the marine Nitrospira sublineage IV identified organisms of this sublineage as main autotrophic nitrite-oxidizers in the investigated brackish biofilter systems.
    PLoS ONE 01/2013; 8(5):e64737. · 3.53 Impact Factor
  • André Lipski, Peter Kämpfer
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    ABSTRACT: Two groups of Gram-negative, aerobic bacterial strains previously isolated from experimental biofilters were investigated to determine their taxonomic position. Based on their 16S rRNA gene sequences, these isolates formed two distinct groups within the genus Aquamicrobium. The gene sequence similarities of the new isolates to the type strains of Aquamicrobium species were below 98.3 %. The presence of ubiquinone-10, C(18 : 1) cis 11 as the predominant fatty acid and a polar lipid pattern with phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and phosphatidylethanolamine was in accordance with the characteristics of this genus. The results of DNA-DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from all recognized species of the genus Aquamicrobium. Therefore, the isolates were assigned to two novel species of this genus for which the names Aquamicrobium ahrensii sp. nov. (type strain 905/1(T) = DSM 19730(T) = CCUG 55251(T)) and Aquamicrobium segne sp. nov. (type strain 1006/1(T) = DSM 19714(T) = CCUG 55250(T)) are proposed. An emended description of the genus Aquamicrobium is also presented.
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 12/2011; 62(Pt 10):2511-6. · 2.11 Impact Factor
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    ABSTRACT: In biofilters of recirculation aquaculture systems (RAS), nitrification by lithoautotrophic microorganisms is essential to prevent the cultivated organisms from intoxication with ammonium and nitrite. In moving-bed biofilters nitrifying microorganisms are immobilized together with heterotrophic bacteria in dense biofilms on carrier elements like plastic beads. Analyses of fatty acid profiles of these biofilms from a marine biofilter revealed a high abundance of Nitrospira-related lipid markers (8-12% of total fatty acids). Further results of a labeling experiment with (13) C-bicarbonate in mineral salts medium with 3 mM nitrite confirmed that Nitrospira is the major autotrophic nitrite oxidizer in the biofilter system. According to 16S rRNA gene sequence analyses the nitrite-oxidizing community in the biofilter consisted of at least two different representatives of Nitrospira, one of which could be successfully isolated. The marine isolate 'Ecomares 2.1' belongs to cluster IVa and showed 98.8% 16S rRNA gene sequence similarity to Nitrospira marina, whereas the enrichment 'M1 marine' is only distantly related (94.0% 16S rRNA gene sequence similarity to N. marina). In laboratory experiments, the isolate exhibited remarkable tolerances against high substrate and product concentrations (30 mM nitrite and 80 mM nitrate) as well as ammonium (50 mM). During the isolation process a strong tendency of this strain to develop biofilms became apparent. Thus, Ecomares 2.1 seems to be well adapted to the attached lifestyle in biofilters and the nitrogenous load prevailing in the effluent waters of RAS. Both members of Nitrospira could be detected by PCR-based methods in environmental samples of marine and brackish RAS biofilters and are therefore considered to be characteristic for these engineered ecosystems.
    Environmental Microbiology 08/2011; 13(9):2536-47. · 6.24 Impact Factor
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    ABSTRACT: A psychrotolerant, Gram-stain-positive, yellow-pigmented, aerobic rod, designated SK1(T), was isolated from a soil sample collected from Store Koldewey, north-east Greenland. Cells were catalase- and methyl red-positive, produced H(2)S and produced acid from glucose, mannitol and salicin. Strain SK1(T) was able to grow between -6 and 28 °C, with an optimum at 20 °C. The isolate contained 2,4-diaminobutyrate, glycine, alanine and glutamic acid in the cell wall and the major menaquinones were MK-10 and MK-11. Identified polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C(15 : 0) (53.5 %), anteiso-C(17 : 0) (17.0 %) and C(18 : 0) (12.1 %). The genomic DNA G+C content was 67.8 mol%. Strain SK1(T) showed the highest 16S rRNA gene sequence similarity with Cryobacterium psychrotolerans 0549(T) (97.6 %) and Cryobacterium roopkundense RuGl7(T) (96.8 %). Considering morphological, physiological, biochemical and chemotaxonomic characters and phylogenetic analysis, strain SK1(T) represents a novel species in the genus Cryobacterium, for which the name Cryobacterium arcticum sp. nov. is proposed. The type strain is SK1(T) ( = DSM 22823(T)  = NCCB 100316(T)).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 08/2011; 61(Pt 8):1849-53. · 2.11 Impact Factor
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    ABSTRACT: A cold-tolerant, yellow-pigmented, Gram-positive, motile, facultatively anaerobic bacterial strain, LI1(T), was isolated from a moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St. Kliment Ohridski. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Leifsonia kafniensis KFC-22(T), Leifsonia pindariensis PON10(T) and Leifsonia antarctica SPC-20(T), with which it showed sequence similarities of 99.0, 97.9 and 97.9 %, respectively. DNA-DNA hybridization revealed a reassociation value of 2.7 % with L. kafniensis LMG 24362(T). The DNA G+C content of strain LI1(T) was 64.5 mol%. The growth temperature range was -6 to 28 °C, with optimum growth at 16 °C. Growth occurred in 0-5 % NaCl and at pH 4.5-9.5, with optimum growth in 1-2 % NaCl and at pH 5.5-6.5. The predominant fatty acids were anteiso-C(15 : 0), C(18 : 0) and iso-C(15 : 0). The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. Physiological and biochemical tests clearly differentiated strain LI1(T) from L. kafniensis. Therefore, a novel cold-tolerant species within the genus Leifsonia is proposed: Leifsonia psychrotolerans sp. nov. (type strain LI1(T) = DSM 22824(T) = NCCB 100313(T)).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 08/2011; 61(Pt 8):1938-43. · 2.11 Impact Factor
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    ABSTRACT: Two novel cold-tolerant, Gram-stain-positive, motile, facultatively anaerobic bacterial strains, LI2(T) and LI3(T), were isolated from moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St Kliment Ohridski. A rod-coccus cycle was observed for both strains. 16S rRNA gene sequence analysis revealed an affiliation to the genus Arthrobacter, with the highest similarity to Arthrobacter stackebrandtii and Arthrobacter psychrochitiniphilus for strain LI2(T) (97.8 and 97.7 % similarity to the respective type strains) and to Arthrobacter kerguelensis and Arthrobacter psychrophenolicus for strain LI3(T) (97.4 and 97.3 % similarity to the respective type strains). The growth temperature range was -6 to 28 °C for LI2(T) and -6 to 24 °C for LI3(T), with an optimum at 16 °C for both strains. Growth occurred at 0-10 % (w/v) NaCl, with optimum growth at 0-1 % (w/v) for LI2(T) and 0.5-3 % (w/v) for LI3(T). The pH range for growth was pH 4-9.5 with an optimum of pH 8 for LI2(T) and pH 6.5 for LI3(T). The predominant fatty acids were anteiso-C(15 : 0), C(18 : 0) and anteiso-C(17 : 0) for LI2(T) and anteiso-C(15 : 0) and C(18 : 0) for LI3(T). Physiological and biochemical tests clearly differentiated strain LI2(T) from A. stackebrandtii and A. psychrochitiniphilus and strain LI3(T) from A. kerguelensis and A. psychrophenolicus. Therefore, two novel species within the genus Arthrobacter are proposed: Arthrobacter livingstonensis sp. nov. (type strain LI2(T)  = DSM 22825(T)  = NCCB 100314(T)) and Arthrobacter cryotolerans sp. nov. (type strain LI3(T)  = DSM 22826(T)  = NCCB 100315(T)).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 04/2011; 61(Pt 4):979-84. · 2.11 Impact Factor
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    ABSTRACT: Geothermal environments are a suitable habitat for nitrifying microorganisms. Conventional and molecular techniques indicated that chemolithoautotrophic nitrite-oxidizing bacteria affiliated with the genus Nitrospira are widespread in environments with elevated temperatures up to 55 °C in Asia, Europe, and Australia. However, until now, no thermophilic pure cultures of Nitrospira were available, and the physiology of these bacteria was mostly uncharacterized. Here, we report on the isolation and characterization of a novel thermophilic Nitrospira strain from a microbial mat of the terrestrial geothermal spring Gorjachinsk (pH 8.6; temperature 48 °C) from the Baikal rift zone (Russia). Based on phenotypic properties, chemotaxonomic data, and 16S rRNA gene phylogeny, the isolate was assigned to the genus Nitrospira as a representative of a novel species, for which the name Nitrospira calida is proposed. A highly similar 16S rRNA gene sequence (99.6% similarity) was detected in a Garga spring enrichment grown at 46 °C, whereas three further thermophilic Nitrospira enrichments from the Garga spring and from a Kamchatka Peninsula (Russia) terrestrial hot spring could be clearly distinguished from N. calida (93.6-96.1% 16S rRNA gene sequence similarity). The findings confirmed that Nitrospira drive nitrite oxidation in moderate thermophilic habitats and also indicated an unexpected diversity of heat-adapted Nitrospira in geothermal hot springs.
    FEMS Microbiology Ecology 02/2011; 75(2):195-204. · 3.56 Impact Factor
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    ABSTRACT: Microorganisms inhabit very different soil habitats in the ice-free areas of Antarctica, playing a major role in nutrient cycling in cold environments. We studied the soil characteristics and the dominant bacterial composition from nine different soil profiles located on Livingston Island (maritime Antarctica). The total carbon (TC) and total nitrogen (TN) values were high for the vegetated soils, decreasing with depth, whereas the values for the mineral soils were generally low. Soil pH was more acidic for moss-covered soils and neutral to alkaline for mineral soils. Numbers of culturable heterotrophic bacteria were higher at vegetated sites, but significant numbers were also detectable in carbon-depleted soils. Patterns of denaturing gradient gel electrophoresis (DGGE) revealed a highly heterogeneous picture throughout the soil profiles. Subsequent sequencing of DGGE bands revealed in total 252 sequences that could be assigned to 114 operational taxonomic units, showing the dominance of members of the Bacteroidetes and Acidobacteria. The results of phospholipid fatty acid analysis showed a lack of unsaturated fatty acids for most of the samples. Samples with a prevalence of unsaturated over saturated fatty acids were restricted to several surface samples. Statistical analysis showed that the dominant soil bacterial community composition is most affected by TC and TN contents and soil physical factors such as grain size and moisture, but not pH.
    FEMS Microbiology Ecology 02/2011; 76(3):476-91. · 3.56 Impact Factor
  • Eva Spieck, André Lipski
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    ABSTRACT: Lithoautotrophic nitrite-oxidizing bacteria (NOB) are known as fastidious microorganisms, which are hard to maintain and not many groups are trained to keep them in culture. They convert nitrite stoichiometrically to nitrate and growth is slow due to the poor energy balance. NOB are comprised of five genera, which are scattered among the phylogenetic tree. Because NOB proliferate in a broad range of environmental conditions (terrestrial, marine, acidic) and have diverse lifestyles (lithoautotrophic, mixotrophic, and heterotrophic), variation in media composition is necessary to match their individual growth requirements in the laboratory. From Nitrobacter and Nitrococcus relatively high cell amounts can be achieved by consumption of high nitrite concentrations, whereas accumulation of cells belonging to Nitrospira, Nitrospina, or the new candidate genus Nitrotoga needs prolonged feeding procedures. Isolation is possible for planktonic cells by dilution series or plating techniques, but gets complicated for strains with a tendency to develop microcolonies like Nitrospira. Physiological experiments including determination of the temperature or pH-optimum can be conducted with active laboratory cultures of NOB, but the attainment of reference values like cell protein content or cell numbers might be hard to realize due to the formation of flocs and the low cell density. Monitoring of laboratory enrichments is necessary especially if several species or genera coexist within the same culture and due to population shifts over time. Chemotaxonomy is a valuable method to identify and quantify NOB in biofilms and pure cultures alike, since fatty acid profiles reflect their phylogenetic heterogeneity. This chapter focusses on methods to enrich, isolate, and characterize NOB by various cultivation-based techniques.
    Methods in enzymology 01/2011; 486:109-30. · 1.90 Impact Factor
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    ABSTRACT: In biofilters of recirculation aquaculture systems (RAS), nitrification by lithoautotrophic microorganisms is essential to prevent the cultivated organisms from intoxication with ammonium and nitrite. In moving‐bed biofilters nitrifying microorganisms are immobilized together with heterotrophic bacteria in dense biofilms on carrier elements like plastic beads. Analyses of fatty acid profiles of these biofilms from a marine biofilter revealed a high abundance of Nitrospira‐related lipid markers (8–12% of total fatty acids). Further results of a labeling experiment with 13C‐bicarbonate in mineral salts medium with 3 mM nitrite confirmed that Nitrospira is the major autotrophic nitrite oxidizer in the biofilter system. According to 16S rRNA gene sequence analyses the nitrite‐oxidizing community in the biofilter consisted of at least two different representatives of Nitrospira, one of which could be successfully isolated. The marine isolate ‘Ecomares 2.1’ belongs to cluster IVa and showed 98.8% 16S rRNA gene sequence similarity to Nitrospira marina, whereas the enrichment ‘M1 marine’ is only distantly related (94.0% 16S rRNA gene sequence similarity to N. marina). In laboratory experiments, the isolate exhibited remarkable tolerances against high substrate and product concentrations (30 mM nitrite and 80 mM nitrate) as well as ammonium (50 mM). During the isolation process a strong tendency of this strain to develop biofilms became apparent. Thus, Ecomares 2.1 seems to be well adapted to the attached lifestyle in biofilters and the nitrogenous load prevailing in the effluent waters of RAS. Both members of Nitrospira could be detected by PCR‐based methods in environmental samples of marine and brackish RAS biofilters and are therefore considered to be characteristic for these engineered ecosystems.
    Environmental Microbiology 01/2011; 13(9). · 6.24 Impact Factor
  • Michèle M Friedrich, André Lipski
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    ABSTRACT: The hexane-degrading bacterial community of a biofilter was characterised by a combination of stable isotope-based phospholipid fatty acid analyses, fluorescence in situ hybridisation and cultivation. About 70 bacterial strains were isolated from a full-scale biofilter used for treatment of hexane containing waste gas of an oil mill. The isolation approach led to 16 bacterial groups, which were identified as members of the Alpha-, Beta- and Gammaproteobacteria, Actinobacteria and Firmicutes. Three groups showed good growth on hexane as the sole source of carbon. These groups were allocated to the genera Gordonia and Sphingomonas and to the Nevskia-branch of the Gammaproteobacteria. Actively degrading populations in the filter material were characterised by incubation of filter material samples with deuterated hexane and subsequent phospholipid fatty acid analysis. Significant labelling of the fatty acids 16:1 cis10, 18:1 cis9 and 18:0 10methyl affiliated the hexane-degrading activity of the biofilter with the isolates of the genus Gordonia. In vitro growth on hexane and in situ labelling of characteristic fatty acids confirmed the central role of these organisms in the hexane degradation within the full-scale biofilter.
    Applied Microbiology and Biotechnology 10/2009; 85(4):1189-99. · 3.81 Impact Factor
  • Michèle M Friedrich, André Lipski
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    ABSTRACT: Two Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from a hexane-treated, full-scale biofilter from an oil mill. The strains were cultivated with hexane as the sole carbon source. One strain, MN154.3(T), showed a fatty acid profile that contained 16 : 0, 18 : 1cis11 and 19 : 0 cyclo11-12 as major compounds, while the second strain, isolate MN28(T), contained 14 : 0 3-OH, 16 : 0 and 18 : 1cis11 as the predominant fatty acids. On the basis of almost-complete 16S rRNA gene sequences, both strains could be allocated to the Nevskia branch of the class Gammaproteobacteria. The sequence similarities for strains MN154.3(T) and MN28(T) with respect to the most closely related type strains of this branch were 90.5 and 94.1 %, respectively. The sequence similarity between strains MN154.3(T) and MN28(T) was 90.6 %. The DNA G+C content of strain MN154.3(T) was 62.8 mol% and that for strain MN28(T) was 64.9 mol%. Both strains possessed ubiquinone-8 as the major quinone. On the basis of the 16S rRNA gene sequences of these two new isolates and several phenotypic differences exhibited with respect to known species of the Nevskia branch, strains MN154.3(T) and MN28(T) represent two novel genera and species, for which the names Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov. are proposed. The type strain of Alkanibacter difficilis gen. nov., sp. nov. is MN154.3(T) (=DSM 14804(T)=LMG 22842(T)) and that of Singularimonas variicoloris gen. nov., sp. nov. is MN28(T) (=DSM 15731(T)=LMG 22844(T)).
    International journal of systematic and evolutionary microbiology 11/2008; 58(Pt 10):2324-9. · 2.11 Impact Factor
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    ABSTRACT: Four Gram-negative, rod-shaped, non-spore-forming and non-motile bacterial strains were isolated from surfaces and biofilms associated with beer-bottling plants. Based on their 16S rRNA gene sequences these isolates were allocated to the genus Chryseobacterium. The sequence similarities of the isolates to the next most closely related type strains of this genus ranged from 96.4 to 98.3%. The presence of menaquinone MK-6 and predominant fatty acids 15:0 iso, 17:1 iso cis9, 15:0 iso 2-OH and 17:0 iso 3-OH supported the affiliation of these strains to the genus. The results of DNA-DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from the next most closely related Chryseobacterium species with validly published names. Therefore, the isolates represent four novel species for which the names Chryseobacterium ureilyticum (type strain F-Fue-04IIIaaaa(T)=DSM 18017(T)=CCUG 52546(T)), Chryseobacterium gambrini (type strain 5-1St1a(T)=DSM 18014(T)=CCUG 52549(T)), Chryseobacterium pallidum (type strain 26-3St2b(T)=DSM 18015(T)=CCUG 52548(T)) and Chryseobacterium molle (type strain DW3(T)=DSM 18016(T)=CCUG 52547(T)) are proposed.
    International journal of systematic and evolutionary microbiology 02/2008; 58(Pt 1):26-33. · 2.11 Impact Factor
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    ABSTRACT: Abstract Permafrost environments,within the Siberian Arctic are natural sources of the climate-relevant trace gas methane. In order to improve our understanding of present and future carbon dynamics in high latitudes, we studied the activity and biomass of the methanogenic,communities,in terrestrial and submarine,permafrost deposits. For these investigations, permafrost cores of Holocene and Late Pleistocene age were drilled in the Laptev Sea region. A high CH4concentration was found in the upper 4 m of the Holocene deposits, which correlates well with the methanogenic activity and biomass. Even the incubation of core material at -3°C and -6°C showed,a significant CH 4 production (range: 0.04–0.78 nmol CH4h ,). The results indicated that the methane,in permafrost,deposits originated from modern methanogenesis by cold-adapted methanogenic archaea. Microbial-generated methane in permafrost sediments is, so far, an underestimated factor for future climate development. Keywords:Laptev Sea; methane; methanogenesis; permafrost deposits; phospholipid biomarker; psychrophiles.
    01/2008;

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174.52 Total Impact Points

Institutions

  • 2011–2014
    • University of Bonn
      • Institute of Nutrition and Food Science (IEL)
      Bonn, North Rhine-Westphalia, Germany
    • Winogradsky Institute Of Microbiology
      Moskva, Moscow, Russia
  • 2011–2013
    • Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research
      Bremerhaven, Bremen, Germany
  • 2007–2011
    • University of Hamburg
      • • Biocenter Klein Flottbek and Botanical Garden (BioZ Flottbek)
      • • Department of Biology
      Hamburg, Hamburg, Germany
  • 1992–2009
    • Universität Osnabrück
      • Microbiology
      Osnabrück, Lower Saxony, Germany