Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments.

Previous investigations of 16S rRNA clone libraries from a wide spectrum of mainly terrestrial origin have shown the worldwide distribution of several as yet uncultivated phylogenetically deeply rooting groups of Actinobacteria. From the percentage of the occurrence of these clones it was concluded that these organisms constitute a significant part of the bacterial microflora in these habitats. Two of the clone groups, previously designated group II and group III, were shown to be phylogenetically moderately related among each other. In order to more exactly determine the abundance of a representative of group II, clone DA079, the fraction of the organism's rRNA in total extracted rRNA was determined in several neighboring samples from Drentse A grassland soil (The Netherlands). The fraction ranged from 2.6 to 9.1%, averaging 5.5%. Based upon comparison of total rRNA and strain DA079-specific rRNA it was concluded that on the average 2 x 10(6) cells/g of this organism are present in the investigated soil. Attempts to isolate members of one of the 16S rDNA clone groups of Actinobacteria were made with samples from a German peat bog, in which the organisms had been detected previously. Molecular detection of group III organisms by a nested PCR approach was possible in different cultivation media. Despite the wide spectrum of growth media employed the isolation of group III strains failed.     

Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species.

In order to assess the effect of genome size and number of 16S rRNA genes (rDNAs) on the quantities of PCR-generated partial 16S rDNA fragments, equimolar amounts of DNA from pairs of different species for which these parameters are known were subjected to gene amplification. The experimentally determined ratio of PCR products obtained, as determined by image analysis of SYBR-Green I-stained amplification products, corresponded well with the predicted ratio calculated from the number of rrn genes per equimolar amounts of DNA in mixtures of Escherichia coli and "Thermus thermophilus" and of Pseudomonas aeruginosa and "T. thermophilus." The values for the pair of Bacillus subtilis and "T. thermophilus" showed greater deviations from the predicted value. The dependence of the amount of 16S rDNA amplification product on these two parameters makes it impossible to quantify the number of species represented in 16S rDNA clone libraries of environmental samples as long as these two parameters are unknown for the species present.     

Prevalence of Schistosoma haematobium Infection among School-Age Children in Afar Area,Northeastern Ethiopia

In this study, the prevalence and intensity of Schistosoma haematobium infection was determined among school-age children living in the Middle and Lower Awash Valley, Afar Regional State of Ethiopia. Between February and May 2014, urine samples were collected from 885 school-age children (5–16 years of age) from the Middle (n = 632; 4 villages) and Lower (n = 253; 3 villages) Awash Valley. All samples were processed using urine filtration to detect and quantify S. haematobium eggs. In addition, a subset of the urine samples was tested for hematuria using a urine dipstick (n = 556). The overall prevalence was 20.8% (95% Confidence Interval (CI) = 18.1%, 23.5%), based on urine filtration but the prevalence considerably varied across villages both in the Middle (from 12.5% to 37.0%) and Lower Awash Valley (from 0 to 5.3%). The overall mean urine egg count (UEC) among the infected children was 4.0 eggs/10 ml of urine (95% CI = 2.43, 5.52). The infection intensity varied from 0.4 eggs/10 ml of urine to 7.7 eggs/10 ml of urine in the Middle Awash Valley, and from 0 to 1.1 eggs/10 ml of urine in Lower Awash Valley. Age and sex were not associated with S. haematobium infection based on the multivariable logistic regression model. The prevalence of hematuria was 56.3% (95% CI = 52.2%, 60.4%) among a subset of the study participants (556) examined using the urine dipstick. The prevalence of hematuria also varies with villages from 8.3% to 93.2%. In conclusion, the prevalence of S. haematobium infection in the Middle Awash Valley was high and it varies across villages. Hence, children living in the present study villages of the Middle Awash Valley need to be treated with praziquantel to reduce morbidity and disrupt transmission.     

Towards a phylogeny of phototrophic purple sulfur bacteria—16S rRNA oligonucleotide cataloguing of 11 species of Chromatiaceae

11 species from 7 genera of Chromatiaceae, depositing sulfur globules inside their cells, were analyzed by comparative oligonucleotide cataloguing of their 16S ribosomal RNA in order to determine the genealogical relationships to each other and to other Gram-negative phototrophic purple and non-phototrophic eubacteria. The rRNA data reveal that members of Chromatium, Amoebobacter, Lamprocystis, Thiocapsa, Thiocystis, Thiodictyon and Thiospirillum form a phylogenetically coherent grouping. The species investigated do not in each case cluster according to their present classification. Organisms storing sulfur inside their cells are moderately related to but clearly separated from members of Ectothiorhodospira, with which they form one of several sublines of group III of phototrophic purple bacteria as defined by Gibson et al. (1979).Dedicated to Professor H. G. Schlegel on the occasion of his 60th birthday.     

Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment.

A molecular ecological study was performed on an Australian soil sample to unravel a substantial portion of the bacterial diversity. A large fragment of the 16S rRNA gene was amplified, using DNA isolated by lysing the microorganisms directly within the soil matrix, and a clone library was generated. Comparative sequence analysis of 30 clones and dot blot hybridization of 83 additional clones with defined oligonucleotide probes revealed the presence of three major groups of prokaryotes of the domain Bacteria. The first one comprises 57 clones that indicate relatives of nitrogen-fixing bacteria of the alpha-2 subclass of the class Proteobacteria; the second group of 7 clones originates from members of the order Planctomycetales that, however, reveal no close relationship to any of the described Planctomycetales species; 22 clones of the third group are indicative of members of a novel main line of descent, sharing a common ancestry with members of planctomycetes and chlamydiae.     

Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences.

The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives. The results of immunological and 5S rRNA studies were confirmed in that the genus is a neighboring taxon of the family Enterobacteriaceae. With regard to the intrageneric structure, Vibrio alginolyticus, Vibrio campbellii, Vibrio natriegens, Vibrio harveyi, Vibrio proteolyticus, Vibrio parahaemolyticus, and Vibrio vulnificus form the core of the genus, while Vibrio (Listonella) anguillarum, Vibrio diazotrophicus, and Vibrio hollisae are placed on the outskirts of the genus. Variable regions around positions 80, 180, and 450 could be used as target sites for genus- and species-specific oligonucleotide probes and polymerase chain reaction primers to be used in molecular identification.     

The phylogenetic position of Streptococcus and Enterococcus

Streptococcus pyogenes, S. equinus, S. bovis, S. salivarius, S. sanguis, S. mutans, S. rattus, S. cricetus, S. lactis, S. raffinolactis and Enterococcus faecalis have been characterized by oligonucleotide cataloguing of their 16S ribosomal RNA. All the organisms form a loose but coherent group that is phylogenetically equivalent to those of lactobacilli, bacilli, the Brochothrix and Listeria group, and related taxa that constitute one of several sublines within the 'Clostridium' branch of Gram-positive eubacteria. Within the Steptococcus-Enterococcus group, organisms fall into three moderately related clusters defined by Enterococcus, the lactic acid streptococci and streptococci of the pyogenic and oral groups, respectively.     

Isolation and characterization of Methanocorpusculum parvum,gen. nov., spec. nov., a new tungsten requiring,coccoid methanogen

A new mesophilic, monotrichously flagellated methane-producing coccus of 1m in diameter was isolated from an anaerobic sour whey digester, originally inoculated with sewage sludge. Growth and methane production were observed with H₂/CO₂, formate and — less effectively — with 2-propanol/CO₂. The isolate grew at temperatures between 15° C and 45° C with the optimum at around 37° C. Acetate, yeast extract and tungstate were required in the medium. Clarified rumen fluid stimulated growth.The DNA of the new methanogen has a G+C content of 48.5 mol%. Comparative 16 S rRNA oligonucleotide cataloguing allows to define the new isolate as a member of a new genus of the order Methanomicrobiales. Further evidence for this is provided by the antigenic crossreactivity with anti-S probes and by metabolic features.Because of its small size the new methanogen is named Methanocorpusculum parvum.This work was supported by a grant of the Deutsche Forschungsgemeinschaft DFG to J. W. and E. S. Immunologic studies were supported in part by grants No. DE-FGO2-84 R 13197 from the U.S. Department of Energy, and No. 261.81/82 from the North Atlantic Treaty Organization (NATO)