Biomedical subjects

Wolf-Rainer Abraham

Publications and source records attributed to Wolf-Rainer Abraham.

18 recordsLinked to original sources

PubMed2007

Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids.

This report is part of a serial study applying stable isotope labelling to rice microcosms to track the utilization of recently photosynthesized carbon by active microbiota in the rhizosphere. The objective of the present study was to apply phospholipid fatty acid-based stable isotope probing (PLFA-SIP) to detect the spatial variation of active microorganisms associated with rhizosphere carbon flow. In total, 49 pulses of 13CO2 were applied to rice plants in a microcosm over a period of 7 days. Rhizosphere soil was separated from bulk soil by a root bag. Soil samples were taken from rhizosphere and bulk soil, and the bulk soil samples were further partitioned both vertically (up layer and down layer) and horizontally with increasing distance to the root bag. Incorporation of 13C into PLFAs sharply decreased with distance to the roots. The labelling of 16:1omega9, 18:1omega7, 18:1omega9, 18:2omega6,9 and i14:0 PLFAs was relatively stronger in the rhizosphere while that of i15:0 and i17:0 increased in the bulk soil. The microorganisms associated with 16:1omega9 were active in both up- and down-layer soils. The microorganisms represented by i14:0, 18:1omega7 and 18:2omega6,9 exhibited a relatively higher activity in up-layer soil, whereas those represented by i15:0 and i17:0 were more active in down-layer soil. These results suggest that in the rhizosphere Gram-negative and eukaryotic microorganisms were most actively assimilating root-derived C, whereas Gram-positive microorganisms became relatively more important in the bulk soil. The active populations apparently differed between up- and down-layer soil and in particular changed with distance to the roots, demonstrating systematic changes in the activity of the soil microbiota surrounding roots.

Biodiversity↗

PubMed2006

Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023(T). Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023(T) was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 degrees Celsius (optimum 15-20 degrees Celsius) and between pH 4.5 and 8.0 (optimum 5.6-6.0). The major phospholipid fatty acid was 18 : 1omega7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023(T) was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA-DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023(T) (=DSM 16100(T)=ATCC BAA-896(T)).

Bacterial Typing Techniques↗

PubMed2006

Controlling biofilms of gram-positive pathogenic bacteria.

Many bacteria can form aggregates on interfaces, called biofilms, where they are much more protected against toxic agents such as antibiotics or antibodies. Bacteria organized in biofilms are therefore very difficult to control and often even high dosages of antibiotics cannot clear infectious biofilms. To form biofilms bacteria have to start a complex genetic program to switch from planktonic to sessile lifestyle. This starts with the determination of their cell density, a process called quorum sensing, triggered by small, water soluble molecules, so called autoinducers. From Gram-positive bacteria several small peptides are known, many of them thiolactones. More recently another group of compounds was discovered probably formed from ribose-homocysteine and the first autoinducer-II identified is a furanosyl borate diester. While small peptides are found to trigger the intraspecies communication autoinducer-II is assumed to be used for communication at the interspecies level. Taking the lead structure from these peptides several derivatives have been developed which prevent biofilm formation in many Gram-positive bacteria, including Staphylococcus aureus. Some of these compounds are already in clinical studies. In this review the different approaches to control bacterial biofilms are discussed together with the difficulties arising from the species-specificity of the autoinducers.

Amino Acid Sequence↗

PubMed2005

Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community.

The naphthalene-degrading activity of a Pseudomonas sp. strain isolated from a creosote-contaminated soil was shown to be encoded by the IncP9 plasmid pNF142 by transfer to Pseudomonas putida KT2442. The effects of the inoculant strain KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community were studied in microcosms with the following treatments: (I) soil, (II) soil with naphthalene, (III) soil with naphthalene and inoculated with KT2442 (pNF142). The inoculant became the dominant bacterial population in treatment (III) as evidenced by cultivation and denaturing gradient gel electrophoresis (DGGE) analysis. The bacterial DGGE profiles revealed drastically reduced complexity due to the numerical dominance of the inoculant. However, group-specific fingerprints (beta-proteobacteria, actinobacteria) that excluded KT2442 (pNF142) showed less severe changes in the bacterial community patterns. A major effect of naphthalene on the soil bacterial community was observed in treatment (II) after 21 days. Two dominant bands appeared whose sequences showed the highest similarity to those of Burkholderia sp. RP007 and Nocardia vinaceae based on 16S rRNA gene sequencing. These bands were less intense in treatment (III). The increased abundance of RP007-like populations due to naphthalene contamination was also confirmed by PCR amplification of the phnAc gene. The nahAc and nahH genes were detected in DNA and cDNA only in treatment III. 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.

Bacteria↗

PubMed2005

Diversity of biphenyl degraders in a chlorobenzene polluted aquifer.

Biphenyl degrading bacteria (40 strains) have been isolated along a gradient of chlorobenzene pollution from an aquifer which did not contain any PCB to answer the question of how metabolic/catabolic abilities exist in ecosystems that have not been stressed with the relevant substrates is important for intrinsic bioremediations. Only few of the isolates were characterized by 16S rRNA gene sequence analyses as Pseudomonas species while the majority were Gram-positive, belonging to the order Actinomycetales and representing the genera Rhodococcus and Arthrobacter. The strains could grow on a variety of chlorobenzoates but no pattern of substrate usage and phylogeny or pollution gradient could be found. Strains which were able to grow on 2,5-dichlorobenzoate were often also able to use 3,4- and 3,5-dichloro- and 2,3,5-trichlorobenzoate or those using 2-chlorobenzoate could usually use 2,6-dichlorobenzoate as well. From that results, it is concluded that a highly diverse, basic metabolic activity for PCB degradation existed at this site despite the absence of PCB.

Biodegradation, Environmental↗

PubMed2005

Brevundimonas mediterranea sp. nov., a non-stalked species from the Mediterranean Sea.

Six strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from the Mediterranean Sea. 16S rRNA gene sequence analysis indicated that the strains were affiliated within the alphaproteobacterial genus Brevundimonas, with Brevundimonas intermedia (99.4 %) and Brevundimonas vesicularis (99.2 %) as their closest relatives. This affiliation was supported by chemotaxonomic data (major polar lipids: phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol; major fatty acids: C(18 : 1), C(16 : 0), C(16 : 1), C(15 : 0), C(17 : 1)omega8c, 11-Me-C(18 : 1)omega5t). The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the strains from all recognized Brevundimonas species. The strains therefore represent a novel species, for which the name Brevundimonas mediterranea sp. nov. is proposed, with the type strain V4.BO.10T)(=LMG 21911T=CIP 107934T).

Caulobacteraceae↗

PubMed2005

Microbial indicator groups in acidic mining lakes.

The salt composition of 14 acidic lakes was analysed, and their microbial communities were compared by their 16S rDNA-based single-strand conformation polymorphism (SSCP) fingerprints. The lakes were grouped into three chemically distinct types, and operational taxonomic units (OTUs) were identified in the 16S rDNA SSCP fingerprints. Discriminant analysis between these groups using a multivariate approach showed that not a single organism, but rather a set of seven OTUs (Ferromicrobium acidophilum, Bacillus pumilus, Acidophilium organovorum, Paenibacillus chibensis, Acidocella sp. and two different alpha-Proteobacteria), was found to be indicative for a given lake type. We conclude that, for these lakes, not single indicator strains but indicator groups exist that are controlled by the ionic composition of the lakes.

Bacteria↗

PubMed2005

Three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water.

Soil contaminated with polychlorinated biphenyls (PCB) was used as an inoculum to grow a complex biofilm community on PCB oil (Aroclor 1242) on a substratum (Permanox). The biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (SSCP), amplicons of the 16S rRNA genes, and chemical analyses of the PCB congeners. SSCP analysis of the young biofilm revealed a rather diverse microbial community with species of the genera Herbaspirillum and Bradyrhizobium as dominant members. The biofilm developing on the PCB droplets displayed pronounced stages of PCB degradation and biofilm development not described before from pure-culture experiments. The first step was the colonization of the substratum while the PCB oil was hardly populated. When a certain density of bacteria was reached on the Permanox, the PCB was colonized, but soon the degradation of the congeners was markedly reduced and many cells were damaged, as seen by LIVE/DEAD staining. Finally, the biofilm formed aggregates and invaded the PCB oil, showing lower numbers of damaged cells than before and a dramatic increase in PCB degradation. This sequence of biofilm formation is understood as a maturation process prior to PCB oil colonization. This is followed by a thin biofilm on the PCB droplet, an aggregation process forming pockets in the PCB, and finally an invasion of the biofilm into the PCB oil. Only the mature biofilm showed degradation of pentachlorinated PCB congeners, which may be reductively dechlorinated and the resulting trichlorobiphenyls then aerobically metabolized.

Bacteria↗

PubMed2004

Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs.

The active bacteria of a biofilm community grown directly on polychlorinated biphenyl (PCB) droplets were analyzed by 16S rRNA fingerprinting, identified by their 16S rRNA gene sequences and fatty acid profiling, and compared with isolates from the biofilm. Although, the multi-species biofilm degraded di- and trichlorinated PCB-congeners these substrates were not attacked by its individual isolated members, which suggests that a metabolic network is responsible for PCB degradation in the biofilm. The community metabolized [U-13C]-2,2'-dichlorobiphenyl incorporating the label into certain phospholipid fatty acids matching those found in Burkholderia species. In contrast, abundant biofilm community members, like Methylobacterium species, did not incorporate the label. These results provide prima faciae evidence for Burkholderia species as the main degraders of PCBs in this type of aerobic soils.

Aerobiosis↗

PubMed2004

Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.

An aerobic, heterotrophic, Gram-negative, curved bacterial strain, designated MIL-1T, was isolated by extinction dilution from an n-tetradecane enrichment culture that was established from sea water/sediment samples collected in the harbour of Milazzo, Italy. In the primary enrichment, the isolate formed creamy-white, medium-sized colonies on the surface of the agar. The isolate did not grow in the absence of NaCl; growth was optimal at 2.7% NaCl. Only a narrow spectrum of organic compounds, including aliphatic hydrocarbons (C7-C20), their oxidized derivatives and acetate, were used as growth substrates. The isolate was not able to grow under denitrifying conditions. The DNA G+C content and genome size of strain MIL-1T were estimated to be 53.2 mol% and 2.2 Mbp, respectively. The major cellular and phospholipid fatty acids were palmitoleic, palmitic and oleic acids (33.5, 29.5 and 11.0% and 18, 32 and 31%, respectively). 3-hydroxy lauric acid was the only hydroxy fatty acid detected. Thirteen different compounds that belonged to two types of phospholipid (phosphatidylethylamine and phosphatidylglycerol) were identified. 16S rRNA gene sequence analysis revealed that this isolate represents a distinct phyletic lineage within the gamma-Proteobacteria and has about 94.4% sequence similarity to Oceanobacter kriegii (the closest bacterial species with a validly published name). The deduced protein sequence of the putative alkane hydrolase, AlkB, of strain MIL-1T is related to the corresponding enzymes of Alcanivorax borkumensis and Pseudomonas oleovorans (81 and 80% similarity, respectively). On the basis of the analyses performed, Thalassolituus oleivorans gen. nov., sp. nov. is described. Strain MIL-1T (=DSM 14913T=LMG 21420T) is the type and only strain of T. oleivorans.

Alkanes↗

PubMed2004

Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov.

The unusually shaped bacteria of the genera Stella, Labrys and Angulomicrobium have been described based on their cell morphology and biochemistry. However, their phylogenetic relationships remain unresolved. An earlier study that was based on 5S rRNA gene sequences placed the genus Stella within the 'Alphaproteobacteria'. In the present report, polar lipids and 16S rRNA genes of the type strains of the two species in the genus Stella, Stella humosa DSM 5900(T) and Stella vacuolata DSM 5901(T), are studied, as well as the type strains of the monospecific genera Labrys (Labrys monachus VKM B-1479(T)) and Angulomicrobium (Angulomicrobium tetraedrale DSM 5895(T)). It was found that the genus Stella belongs to the order Rhodospirillales in the family Rhodospirillaceae, and not to the Acetobacteraceae. Whilst the position of the genus Angulomicrobium in the family Hyphomicrobiaceae was confirmed, the genus Labrys could not be placed into any known family, but was adjacent to the family 'Beijerinckiaceae'. In addition, data were obtained for strain VKM B-1336, which was shown not to belong to the genus Angulomicrobium, and strain NCIMB 1785(T) (=DSM 15561(T)), for which the name Angulomicrobium amanitiforme sp. nov. is proposed.

Acetobacteraceae↗

PubMed2004

Phylogeny of the ring-forming bacterium Arcicella aquatica gen. nov., sp. nov. (ex Nikitin et al. 1994), from a freshwater neuston biofilm.

Arcicella aquatica NO-502(T), obtained from a neuston film on a freshwater lake and belonging to the phylum Bacteroidetes, is characterized by ring-forming cells. The bacterium is a strict aerobe, with optimal growth between 28 and 30 degrees C. Carbohydrates, but no organic acids or amino acids, are used as substrates. The G+C content of strain NO-502(T) is 34.5 mol%; its genome size is 2.9 x 10(9) Da. The genus Arcicella and its type species Arcicella aquatica (type strain NO-502(T)=LMG 21963(T)=CIP 107990(T)) are proposed, and descriptions of this genus and species are given.

Base Composition↗

PubMed2004

Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids.

Two cauliform bacteria (CM243T and CM251) isolated by J. Poindexter from the Atlantic Ocean were characterized by 16S rRNA gene sequencing, TaqI restriction fragment length polymorphism and single-strand conformation polymorphism analyses of the internally transcribed 16S-23S rDNA spacer (ITS1) region, analysis of fatty acids from cellular lipids, mass spectrometry of polar lipids and physiological properties. The two strains showed very low diversity of polar lipids with diacyl-sulfoquinovosyl glycerols as the predominant lipids. The two bacterial strains were observed to have nearly identical 16S rRNA gene sequences and could not be differentiated by their ITS1 regions. The isolates differed from species of the genus Maricaulis by their 16S rRNA gene sequences, polar lipids and fatty acid patterns. On the basis of the genotypic analyses and estimations of phylogenetic similarities, physiological and chemotaxonomic characteristics, it is proposed that the isolates represent a new genus and species, for which the name Woodsholea maritima gen. nov., sp. nov. (type strain CM243T=VKM B-1512T=LMG 21817T) is proposed.

Atlantic Ocean↗

PubMed2003

Assimilation of toluene carbon along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids.

A food chain consisting of toluene, toluene-degrading Pseudomonas sp. PS+ and a bacterivorous flagellated amoebae Vahlkampfia sp. was established in a batch culture. This culture was amended with [U-13C]toluene and served as a model system to elucidate the flux of carbon in the food chain by quantifying bacterial biovolumes and 13C enrichment of phospholipid fatty acid (PLFA) biomarkers of the bacteria and the heterotrophic protists. Major PLFA detected in the batch co-culture included those derived from Pseudomonas sp. PS+ (16:1omega7c and 18:1omega7c) and Vahlkampfia sp. (20:4omega6c and 20:3omega6c). A numerical model including consumption of toluene by the bacteria and predation of the bacteria by the heterotrophic protists was adjusted to the measured toluene carbon, bacterial carbon and delta13C values of bacterial and protist biomass. Using this model, we estimated that 28+/-7% of the consumed toluene carbon was transformed into bacterial biomass, and 12+/-4% of the predated bacterial carbon was incorporated into heterotrophic protist biomass. Our study showed that the 13C enrichment of PLFA biomarkers coupled to biomass determination via biovolume calculations is a suitable method to trace carbon fluxes in protist-inclusive microbial food chains because it does not require the separation of protist cells from bacterial cells and soil particles.

Amoeba↗

PubMed2003

Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water.

The taxonomic characteristics of two bacterial strains, RB-8(T) and RB-9, isolated from hydrocarbon-degrading enrichment cultures obtained from Antarctic coastal marine environments (Rod Bay, Ross Sea), were determined. These bacteria were psychrophilic, aerobic and Gram-negative with polar flagella. Growth was not observed in the absence of NaCl, occurred only at concentrations of Na+ above 20 mM and was optimal at an NaCl concentration of 3-5% (w/v). The major cellular fatty acids were monounsaturated straight-chain fatty acids. The strains were able to synthesize the polyunsaturated fatty acid eicosapentaenoic acid (20: 5omega3) at low temperatures. The DNA G + C contents were 41-42 mol%. The strains formed a distinct phyletic line within the gamma-Proteobacteria, with less than 89.6% sequence identity to their closest relatives within the Bacteria with validly published names. Both isolates exhibited a restricted substrate profile, with a preference for aliphatic hydrocarbons, that is typical of marine hydrocarbonoclastic micro-organisms such as Alcanivorax, Marinobacter and Oleiphilus. On the basis of ecophysiological properties, G + C content, 16S rRNA gene sequences and fatty acid composition, a novel genus and species within the gamma-Proteobacteria are proposed, Oleispira antarctica gen. nov., sp. nov.; strain RB-8(T) (= DSM 14852(T) = LMG 21398(T)) is the type strain.

Aerobiosis↗

PubMed2003

Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech.

Five bacterial strains were isolated from a non-toxigenic strain of the marine dinoflagellate Alexandrium tamarense (Lebour) Balech CCMP 116 (NEPCC C116), during a survey of the diversity of bacteria associated with paralytic shellfish toxin-producing cultures of Alexandrium spp. (Dinophyta). All strains were strictly aerobic, Gram-negative, straight or curved rods. Cells were dimorphic, with stalks (or prosthecae) and non-motile or non-stalked and motile, by means of a single polar flagellum. The bacteria grew best at salt concentrations ranging from 2 to 10 % and growth occurred at 10 degrees C, but not at 50 degrees C. The G+C content of the chromosomal DNA of the strains was determined to be 61-62 mol%. Major cellular fatty acids of the bacteria presented a unique profile. 16S rRNA gene sequence analysis showed the five strains to be related to genera of budding bacteria of marine origin in the 'Alphaproteobacteria', namely, Hirschia, Maricaulis and Hyphomonas, although they exhibited substantial differences in morphology, substrate utilization and fatty acid profile to members of these genera. The five strains are proposed to comprise a new species of a new genus, Oceanicaulis alexandrii gen. nov., sp. nov., the type strain of which is C116-18(T) (=DSM 11625(T)=NCIMB 13905(T)).

Animals↗

PubMed2002

Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.

A bacterial isolate, ME102T, was obtained from an n-hexadecane enrichment culture of seawater/sediment samples collected in the harbour of Messina (Italy). This gram-negative, aerobic, motile, rod-shaped bacterium used a narrow spectrum of organic compounds, including aliphatic hydrocarbons, alkanoates and alkanoles, as carbon and energy sources. None of the sugars, organic acids or amino acids tested was used. During cultivation on n-alkanes as the sole source of carbon and energy, the cells formed a biofilm on the surface of the alkane droplets. Large-scale (sometimes >50% of the cell mass) intracellular accumulation of alkanoates occurred in cells adsorbed on the alkane surface and under nitrogen-limiting conditions. 16S rRNA gene sequence analysis showed that this isolate represents a distinct lineage in the gamma-Proteobacteria and has about 91% sequence identity to members of Marinobacter and Alcanivorax, the closest genera. Four different types of polar lipid could be detected, phosphatidyl glycerol, phosphatidyl ethylamine, phosphatidyl dimethylethylamine and lipids belonging to an unknown type of phospholipid (m/z between 861 and 879). The principal fatty acids in the polar lipid fatty acid profile were 16:0 and 16:1. The putative gene encoding the key enzyme of alkane catabolism, alkane hydroxylase (AlkB), has been cloned. The protein sequence of the putative AlkB of the isolate ME102T was related to the AlkB of Pseudomonas oleovorans and Alcanivorax borkumensis, showing about 60% sequence identity. On the basis of physiological studies and taking into account the distant phylogenetic position of isolate ME102T relative to previously described organisms, a novel genus and species is proposed, Oleiphilus messinensis gen. nov., sp. nov., within a new family, Oleiphilaceae fam. nov. Strain ME102T (= DSM 13489T = LMG 20357T) is the type and only strain of O. messinensis.

Alkanes↗

PubMed2002

Phylogeny of Maricaulis Abraham et al. 1999 and proposal of Maricaulis virginensis sp. nov., M. parjimensis sp. nov., M. washingtonensis sp. nov. and M. salignorans sp. nov.

Thirteen marine bacteria isolated from different locations, belonging to the genus Maricaulis, were characterized by 16S rRNA gene sequencing, DNA-DNA hybridizations and analysis of the internally transcribed 16S-23S rDNA spacer (ITS1) region, analysis of fatty acids from total lipids, mass spectrometry of polar lipids and determination of temperature and NaCl tolerances. The data obtained led to the identification of five new sulfoquinovosyl diacylglycerols, using tandem mass spectrometry, and the fragmentation patterns of the individual compounds. Four novel species were identified and described as Maricaulis virginensis sp. nov. (type strain VKM B-1 5139T)), Maricaulis parjimensis sp. nov. (type strain MCS 25(T)), Maricaulis washingtonensis sp. nov. (type strain MCS 6(T)) and Maricaulis salignorans sp. nov. (type strain MCS 18(T)). They differ in their temperature and salt tolerances and can be differentiated by their polar lipids and fatty acid patterns, as well as their ITS1 and 16S rRNA gene sequences.

Alphaproteobacteria↗