Publications

cultivation of cilia-associated respiratory bacillus in artificial medium and determination of the 16s rrna gene sequence.	cilia-associated respiratory (car) bacillus, an unclassified gliding bacterium associated with respiratory disease in rats, mice, and rabbits, has previously been cultivated only in embryonated chicken eggs, cell culture, or cell culture medium supplemented with conditioned medium from cultured tracheas. a reference strain of car bacillus, originally isolated in eggs, grew in cell culture flasks as adherent individual bacilli and ropy, whorled fascicles in cell culture media supplemented only wi ...	1993	7504686
natural pathogens of laboratory mice, rats, and rabbits and their effects on research.	laboratory mice, rats, and rabbits may harbor a variety of viral, bacterial, parasitic, and fungal agents. frequently, these organisms cause no overt signs of disease. however, many of the natural pathogens of these laboratory animals may alter host physiology, rendering the host unsuitable for many experimental uses. while the number and prevalence of these pathogens have declined considerably, many still turn up in laboratory animals and represent unwanted variables in research. investigators ...	1998	9564563
molecular characterization of epiphytic bacterial communities on charophycean green algae	epiphytic bacterial communities within the sheath material of three filamentous green algae, desmidium grevillii, hyalotheca dissiliens, and spondylosium pulchrum (class charophyceae, order zygnematales), collected from a sphagnum bog were characterized by pcr amplification, cloning, and sequencing of 16s ribosomal dna. a total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. by phyloge ...	1998	9797295
identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing.	bacteria with limited genomic cross-hybridization were isolated from soil contaminated with c5+, a mixture of hydrocarbons, and identified by partial 16s rrna sequencing. filters containing denatured genomic dnas were used in a reverse sample genome probe (rsgp) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [dcpd]) on community composition. hybridization with labeled total-community dna isolated from soil exp ...	1998	16349504
molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities.	petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 10(6) microorganisms ml(-1), a density 100 times higher than the densities in groundwater around the cavities (control groundwater). to characterize bacterial populations growing in the cavity groundwater, 46 pcr-amplified almost full-length 16s ribosomal dna (rdna) fragments were cloned and sequenced, and 28 different sequences were obtained. all of the sequences wer ...	2000	11055927
phylogenetic characterization and in situ detection of a cytophaga-flexibacter-bacteroides phylogroup bacterium in tuber borchii vittad. ectomycorrhizal mycelium.	mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. in this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus tuber borchii vittad. universal eubacterial primers specific for the 5' and 3' ends of the 16s rrna gene (16s rdna) were used for pcr ampli ...	2000	11055961
comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria.	in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ...	2000	11055963
composition of soil microbial communities enriched on a mixture of aromatic hydrocarbons.	soil contaminated with c5+, which contained benzene (45%, wt/wt), dicyclopentadiene (dcpd) plus cyclopentadiene (together 20%), toluene (6%), styrene (3%), xylenes (2%), naphthalene (2%), and smaller quantities of other compounds, served as the source for isolation of 55 genomically distinct bacteria (standards). use of benzene as a substrate by these bacteria was most widespread (31 of 44 standards tested), followed by toluene (23 of 44), xylenes (14 of 44), styrene (10 of 44), and naphthalene ...	2000	11097903
succession of indigenous pseudomonas spp. and actinomycetes on barley roots affected by the antagonistic strain pseudomonas fluorescens dr54 and the fungicide imazalil.	in recent years, the interest in the use of bacteria for biological control of plant-pathogenic fungi has increased. we studied the possible side effects of coating barley seeds with the antagonistic strain pseudomonas fluorescens dr54 or a commercial fungicide, imazalil. this was done by monitoring the number of indigenous pseudomonas organisms and actinomycetes on barley roots during growth in soil, harvest after 50 days, and subsequent decomposition. bacteria were enumerated by traditional pl ...	2001	11229904
predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture.	we investigated whether individual populations of freshwater bacteria in mixed experimental communities may exhibit specific responses to the presence of different bacterivorous protists. in two successive experiments, a two-stage continuous cultivation system was inoculated with nonaxenic batch cultures of the cryptophyte cryptomonas sp. algal exudates provided the sole source of organic carbon for growth of the accompanying microflora. the dynamics of several 16s rrna-defined bacterial populat ...	2001	11319094
effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rrna gene in pcr-based microbial community analyses and genetic profiling.	genetic profiling techniques of microbial communities based on pcr-amplified signature genes, such as denaturing gradient gel electrophoresis or single-strand-conformation polymorphism (sscp) analysis, are normally done with pcr products of less than 500-bp. the most common target for diversity analysis, the small-subunit rrna genes, however, are larger, and thus, only partial sequences can be analyzed. here, we compared the results obtained by pcr targeting different variable (v) regions (v2 an ...	2001	11472932
bacteria and archaea physically associated with gulf of mexico gas hydrates.	although there is significant interest in the potential interactions of microbes with gas hydrate, no direct physical association between them has been demonstrated. we examined several intact samples of naturally occurring gas hydrate from the gulf of mexico for evidence of microbes. all samples were collected from anaerobic hemipelagic mud within the gas hydrate stability zone, at water depths in the ca. 540- to 2,000-m range. the delta(13)c of hydrate-bound methane varied from -45.1 per thous ...	2001	11679338
new degenerate cytophaga-flexibacter-bacteroides-specific 16s ribosomal dna-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon.	river microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. in this study the bacterial diversity of river taff epilithon in south wales was investigated. a 16s ribosomal dna (rdna) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. the epilithon was found to be very diverse, with an estimated 59.6% of the bacteri ...	2002	11772628
extensive profiling of a complex microbial community by high-throughput sequencing.	complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. the availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. here we describe the application of an e ...	2002	12039767
evidence for natural horizontal transfer of the pcpb gene in the evolution of polychlorophenol-degrading sphingomonads.	the chlorophenol degradation pathway in sphingobium chlorophenolicum is initiated by the pcpb gene product, pentachlorophenol-4-monooxygenase. the distribution of the gene was studied in a phylogenetically diverse group of polychlorophenol-degrading bacteria isolated from contaminated groundwater in kärkölä, finland. all the sphingomonads isolated were shown to share pcpb gene homologs with 98.9 to 100% sequence identity. the gene product was expressed when the strains were induced by 2,3,4,6-te ...	2002	12200305
diversity and succession of the intestinal bacterial community of the maturing broiler chicken.	the diversity of bacterial floras in the ilea and ceca of chickens that were fed a vegetarian corn-soy broiler diet devoid of feed additives was examined by analysis of 1,230 partial 16s rrna gene sequences. nearly 70% of sequences from the ileum were related to those of lactobacillus, with the majority of the rest being related to clostridiaceae (11%), streptococcus (6.5%), and enterococcus (6.5%). in contrast, clostridiaceae-related sequences (65%) were the most abundant group detected in the ...	2003	14602645
integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution.	integrons are horizontal gene transfer (hgt) systems containing elements necessary for site-specific recombination and expression of foreign dna. the overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. this report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. first, using culture-independent techniques, we explored the diversity of integrons and integron-tran ...	2004	14766601
elucidating the key member of a linuron-mineralizing bacterial community by pcr and reverse transcription-pcr denaturing gradient gel electrophoresis 16s rrna gene fingerprinting and cultivation.	a bacterial community from danish agricultural soil was enriched with linuron [n-(3,4-dichlorophenyl)-n'-methoxy-n'-methylurea] as the sole carbon and nitrogen source. the community mineralized [ring-u-14c]linuron completely to 14co2 and 14c-biomass. denaturing gradient gel electrophoresis analysis and cultivation revealed that a variovorax sp. was responsible for the mineralization activity.	2005	16000836
community structure and diversity of biofilms from a beer bottling plant as revealed using 16s rrna gene clone libraries.	the microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16s rrna genes. clone libraries were differentiated by amplified 16s rrna gene restriction analysis and representative clones from each group were sequenced. the diversity of the clone libraries was comparable with the diversity found for environmental samples. no evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that bio ...	2005	16204578
composition and dynamics of bacterial communities of a drinking water supply system as assessed by rna- and dna-based 16s rrna gene fingerprinting.	bacterial community dynamics of a whole drinking water supply system (dwss) were studied from source to tap. raw water for this dwss is provided by two reservoirs with different water characteristics in the harz mountains of northern germany. samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. rna and dna were extracted from the sampled water. the 16s rrna or its gen ...	2006	16517632
selective phylogenetic analysis targeted at 16s rrna genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments.	deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16s rrna gene clone library analysis. to eliminate possible contamination by pcr-amplified 16s rrna genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the g+c content of the 16s rrna gene and the o ...	2006	16391020
cultivation-independent methods applied to the microbial prospection of oil and gas in soil from a sedimentary basin in brazil.	the upper parts of oil field structures may leak gas which is supposed to be indirectly detected by the soil bacterial populations. such microorganisms are capable of consuming this gas, supporting the microbial prospection of oil and gas (mpog) methodology. the goal of the present work was to characterize microbial communities involved in short-chain alkane metabolism, namely methane, ethane and propane, in samples from a petroliferous (p) soil through clone libraries of the 16s rrna gene of th ...	2011	22018208
microbial survey of a full-scale, biologically active filter for treatment of drinking water.	the microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. nitrosomonas, nitrospira, sphingomonadales, and rhizobiales dominated the clone libraries. the results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.	2012	22752177
microbial diversity in the floral nectar of seven epipactis (orchidaceae) species.	floral nectar of animal-pollinated plants is commonly infested with microorganisms, yet little is known about the microorganisms inhabiting the floral nectar of orchids. in this study, we investigated microbial communities occurring in the floral nectar of seven epipactis (orchidaceae) species. culturable bacteria and yeasts were isolated and identified by partially sequencing the small subunit (ssu) ribosomal rna (rrna) gene and the d1/d2 domains of the large subunit (lsu) rrna gene, respective ...	2013	23836678
biochemistry and genetics of acc deaminase: a weapon to "stress ethylene" produced in plants.	1-aminocyclopropane-1-carboxylate deaminase (accd), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. owing to accd activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. accd breaks down acc, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. acc deam ...	2015	26441873