André Lipski

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

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Publications (63)195.02 Total impact

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    ABSTRACT: The aim of this study was to develop a repeatable method for the measurement of microbial load reduction factors after hand and machine dishwashing processes that meet the requirements associated with consumer studies, based on non-pathogen test strains. Microorganisms were isolated from tableware, identified and cultured for this purpose, mixed with soiling agents and lyophilised for storage purposes. Detailed instructions for ambient conditions and disinfection, and preparation and application of soiling agents were defined. The method chosen in this study successfully led to repeatable results. The food matrix of the soiling agents used for the application of test strains shows to have a large impact. This is, therefore, the first repeatable method that enables the comparison of microbial load reduction factors after machine with hand dishwashing. In addition, the method was designed in a way that enables further consumer studies.
    No preview · Article · May 2015 · Tenside Surfactants Detergents
  • Mareike Weber · Janina Geißert · Myriam Kruse · André Lipski
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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.
    No preview · Article · Sep 2014 · Journal of Dairy Science
  • Sandra Szczepanski · André Lipski
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    ABSTRACT: Essential oils are promising natural ingredients for the food industry due to their preservative and antimicrobial effects. We analysed the inhibiting effects of thyme, oregano and cinnamon essential oil at sublethal concentrations on biofilm formation of three biofilm forming bacterial strains. These strains of the genera Acinetobacter, Sphingomonas and Stenotrophomonas were isolated from authentic biofilms in the food industry during a previous study. Minimal inhibitory concentrations (MIC's) for growth and biofilm forming activity were tested in a 96-well microtiter plate assay. For two out of three strains we found an inhibiting effect of essential oils on biofilm formation below the minimal inhibitory concentration (MIC) for growth of these strains. In contrast, for one strain inhibition of growth and inhibition of the biofilm formation by the essential oils are initiated at the same concentration. Thyme oil was capable to inhibit the development of a biofilm at sublethal concentrations at 0.001% (w/v). This oil seems to be a more efficient specific inhibitor compared with the other tested essential oils against the biofilm formation of all tested isolates. Controls showed that the detergent used, Tween 20, was not responsible for this effect. Structural changes of the biofilms after exposition to sublethal concentrations of essential oils were confirmed by fluorescence microscopy.
    No preview · Article · Feb 2014 · Food Control
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    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).
    Preview · Article · Jan 2014 · International Journal of Systematic and Evolutionary Microbiology
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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.
    No preview · Article · Aug 2013 · Systematic and Applied Microbiology
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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.
    Full-text · Article · Aug 2013 · International Journal of Systematic and Evolutionary Microbiology
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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.
    Full-text · Article · May 2013 · PLoS ONE
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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).
    Full-text · Article · Mar 2013 · International Journal of Systematic and Evolutionary Microbiology
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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).
    Full-text · Article · Jan 2013 · International Journal of Systematic and Evolutionary Microbiology
  • 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.
    No preview · Article · Dec 2011 · Methods in enzymology
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    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.
    Preview · Article · Dec 2011 · International Journal of Systematic and Evolutionary Microbiology
  • Sabine Keuter · Myriam Kruse · André Lipski · Eva Spieck
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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.
    No preview · Article · Aug 2011 · Environmental Microbiology
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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)).
    Full-text · Article · Aug 2011 · International Journal of Systematic and Evolutionary Microbiology
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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)).
    Full-text · Article · Aug 2011 · International Journal of Systematic and Evolutionary Microbiology
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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)).
    Full-text · Article · Apr 2011 · International Journal of Systematic and Evolutionary Microbiology
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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.
    Full-text · Article · Feb 2011 · FEMS Microbiology Ecology
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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.
    Full-text · Article · Feb 2011 · FEMS Microbiology Ecology
  • Sabine Keuter · Myriam Kruse · André Lipski · Eva Spieck
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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.
    No preview · Article · Jan 2011 · Environmental Microbiology
  • 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.
    No preview · Article · Oct 2009 · Applied Microbiology and Biotechnology
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    ABSTRACT: Gypsum crusts containing multicolored, stratified microbial communities develop in the evaporation ponds of a commercial saltern in Eilat, Israel at salt concentrations between 190 and 240gl−1. The upper 0.5–2cm of the crust is densely populated by orange-brown unicellular cyanobacteria. Below, a layer of green-colored filamentous cyanobacteria is found. Underneath, a bright purple layer of anoxygenic phototrophs is present, below which a reduced black layer is found. We have investigated the biological properties of this crust using a wide variety of techniques, and we here review the results of these interdisciplinary studies. The tests performed included microscopic examination of the biota, phylogenetic analyses based on 16S rRNA gene clone libraries and denaturing gradient gel electrophoresis, fatty acid analysis, light intensity and light quality measurements, microelectrode studies of oxygen profiles and oxygen evolution, determination of sulfate reduction using radioisotope methods, and measurement of methane evolution. The stable vertical stratification in the system enabled separate analyses of the different layers with a high spatial resolution. It was therefore possible to combine the different approaches and obtain information on the activities of the different types of oxygenic and anoxygenic phototrophs, dissimilatory sulfate reducers and methanogens in the different layers, as well as phylogenetic information on the nature of the microorganisms responsible for these processes. The gypsum crust thus becomes a paradigm for the study of a wide variety of microbial processes and their interrelationships in the presence of high salt concentrations.
    Full-text · Article · Jun 2009 · Hydrobiologia