Genetic structure and phylogenetic relationships of Ralstonia solanacearum strains from diverse origins in Guangdong Province,China

Bacterial wilt, caused by Ralstonia solanacearum species complex is a key yield‐limiting factor on crops in Guangdong province, China. The genetic diversity of 110 R. solanacearum strains collected from 16 host plants in different areas of Guangdong province was analysed using biovar and phylotype classification schemes. Of 110 strains, fifty‐five strains belong to biovar 3, fifty‐two strains belong to biovar 4, two strains belong to biovar 2 and one strain belonged to biovar 1. Phylotype‐specific multiplex PCR showed that 108 strains belonged to phylotype I (biovars 1, 3, 4) and two strains belonged to phylotype II (biovar 2). The result of phylogenetic relationships analysis based on egl gene sequences demonstrated that 108 strains of phylotype I were grouped into nine previously described sequevars and a new sequevar 57, and two strains of phylotype II were grouped into sequevar 1. Sequevars 15, 34 and 44 widely distributed in Guangdong were predominant sequevars. Sequevar 45 was first reported on potato and pumpkin in China. These results revealed the genetic structure and phylogenetic relationships of R. solanacearum population in Guangdong and will be helpful in bacterial wilt‐resistance breeding.     

Development of asymmetry in the caenogastropods Amphissa columbiana and Euspira lewisii

Abstract. The asymmetry displayed by the body plan of gastropods has been directly or indirectly attributed to an evolutionary process called torsion. Torsion is defined as a rotation of 180° between the cephalopodium (head and foot) and visceropallium (visceral organs, mantle, mantle cavity, and shell). During development, the displacement of anatomical components occurs during a process called "ontogenetic torsion." Although ontogenetic torsion is central to theories of gastropod evolution, surprisingly few studies have documented actual tissue movements during the development of asymmetry in gastropods. We investigated the development of the mantle cavity and pleurovisceral nerve connective (visceral nerve loop) in the caenogastropods Amphissa columbiana and Euspira lewisii , because displacements of both of these structures are interpreted as major consequences of torsion. Scanning electron micrographs, histological sections, and immunofluorescence images showed that the developing vis-ceropallium twists by 90° relative to the cephalopodium, the mantle cavity initially forms on the right side, and displacements of the visceral nerve loop become evident on the left side before the right side. A developmental stage in which the mantle cavity is confined to the right side has also been reported in members of the Vetigastropoda and Heterobranchia. We suggest that further comparative studies should test the hypothesis that early development throughout the Gastropoda converges on an embryonic organization in which the mantle cavity and anus are located laterally, despite clade-specific differences in developmental patterns both before and after this stage.     

Biofilm formation by avian Escherichia coli in relation to media, source and phylogeny

AIMS: To assess the abilities of 105 avian pathogenic Escherichia coli (APEC) and 103 avian faecal commensal E. coli (AFEC) to form biofilms on a plastic surface and to investigate the possible association of biofilm formation with the phylotype of these isolates. METHODS AND RESULTS: Biofilm production was assessed in 96-well microtitre plates using three different media, namely, M63 minimal medium supplemented with glucose and casamino acids, brain-heart infusion broth, and diluted tryptic soy broth. Avian E. coli are highly variable in their ability to form biofilms. In fact, no strain produced a strong biofilm in all three types of media; however, most (75.7% AFEC and 55.2% APEC) were able to form a moderate or strong biofilm in at least one medium. Biofilm formation in APEC seems to be mostly limited to nutrient deplete media; whereas, AFEC are able to form biofilms in both nutrient deplete and replete media. Also, biofilm formation in E. coli from phylogenetic groups B2, D and B1 was induced by nutrient deplete conditions; whereas, biofilm formation by members of phylogenetic group A was strongest in a rich medium. CONCLUSIONS: Biofilm formation by APEC and phylotypes B2, D and B1 is induced by nutrient deplete conditions, while AFEC are able to form biofilms in both nutrient rich and deplete media. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to investigate biofilm formation by a large sample of avian E. coli isolates, and it provides insight into the conditions that induce biofilm formation in relation to the source (APEC or AFEC) and phylogenetic group (A, B1, B2 and D) of an isolate.     

Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self‐organizing map (SOM)

Aims: To determine the origins of DNA sequences isolated from the rumen microbial ecosystem using a self‐organizing map (SOM). Methods and Results: DNA sequences other than 16S small subunit ribosomal RNA (SSU rRNA) gene sequences that were detected from the rumen were analysed by the SOM method reported by Abe et al. [2000, Self‐Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 365, 27–34]. Because query sequences positioned by SOM were scattered on the master drawing of SOM, it was suggested that many DNA sequences isolated from the rumen were collected from a broad range of micro‐organisms. Although the results obtained by SOM were similar to those obtained by the neighbour‐joining (NJ) method, SOM was able to presume the phylotypes of the query sequences without information about the 16S SSU rRNA gene sequences and homology searches, and to reveal existence of novel micro‐organisms deduced to be cellulolytic bacteria, archaea and methanotrophic bacterium. Conclusions: As the SOM method defined phylotypes of unreported rumen micro‐organisms, it is presumed that these phylotypes would be involved in rumen fermentation in cooperation with known rumen micro‐organisms. Moreover, it is demonstrated that SOM is a useful tool for affiliating DNA sequences, which have no matches in databases. Significance and Impact of Study: Through SOM analysis, a better means of identifying rumen micro‐organisms and estimating their roles in rumen function was provided.     

Genomic sequencing of two isolates of Ralstonia solanacearum causing Sergipe facies and comparative analysis with Bugtok disease isolates

Ralstonia solanacearum is the causal agent of Moko disease in bananas, which in the state of Sergipe in northeastern Brazil causes “Sergipe facies”. This disease induces atypical symptoms similar to those of Bugtok disease in the Philippines. This study was conducted to sequence, assemble, and annotate the genomes of the Sergipe facies-causing isolates SFC and IBSBF2570 (sequevar IIA-53) and compare their genomes with two representative isolates causing Bugtok disease. The genomes were sequenced and assembled, resulting in lengths of 5.58 Mb (SFC) and 5.46 Mb (IBSBF2570) in 185 and 174 contigs, respectively. The isolates of Sergipe facies and Bugtok disease showed similarities in their gene contents. We identified 5,668 information clusters, 3,752 of which were shared by all genomes (core genes). Moreover, 3,585 single-copy genes were identified. Isolates causing Bugtok disease exclusively shared 266 more information clusters than the isolates causing Sergipe facies. These results suggest that Sergipe facies and Bugtok disease isolates show high genomic similarity. However, the similarity is even greater between the Bugtok disease isolates. This may be because of their longer period of interaction compared to Sergipe facies isolates.     

Global biogeography of SAR11 marine bacteria

The ubiquitous SAR11 bacterial clade is the most abundant type of organism in the world's oceans, but the reasons for its success are not fully elucidated. We analysed 128 surface marine metagenomes, including 37 new Antarctic metagenomes. The large size of the data set enabled internal transcribed spacer (ITS) regions to be obtained from the Southern polar region, enabling the first global characterization of the distribution of SAR11, from waters spanning temperatures ?2 to 30°C. Our data show a stable co‐occurrence of phylotypes within both ‘tropical’ (>20°C) and ‘polar’ (<10°C) biomes, highlighting ecological niche differentiation between major SAR11 subgroups. All phylotypes display transitions in abundance that are strongly correlated with temperature and latitude. By assembling SAR11 genomes from Antarctic metagenome data, we identified specific genes, biases in gene functions and signatures of positive selection in the genomes of the polar SAR11—genomic signatures of adaptive radiation. Our data demonstrate the importance of adaptive radiation in the organism's ability to proliferate throughout the world's oceans, and describe genomic traits characteristic of different phylotypes in specific marine biomes.     

Detection of novel oral phylotypes associated with periodontitis

A phylogenetic approach based on 16S rRNA (rDNA) has been recently applied to investigate the diversity of cultivable and uncultivable species in the human oral cavity without cultivation. In a previous study [Sakamoto et al. (2000) Microbiol. Immunol. 44, 643-652], we identified a number of novel oral phylotypes, representing as yet uncultured organisms. The purpose of this study was to design specific PCR primers for five phylotypes AP12, AP21, AP24, AP50, and RP58, which are deeply branched particularly in the phylogenetic tree, and determine the prevalence of these phylotypes in 45 patients with periodontitis and 18 healthy subjects. The specificity of each primer was validated by the sequence analysis of PCR products obtained from saliva and subgingival plaque samples. Among phylotypes tested, phylotype AP24, which is closely related to oral clone DA014 reported previously [Paster et al. (2001) J. Bacteriol. 183, 3770-3783], was significantly associated with saliva and subgingival plaque samples from patients with periodontitis (P<0.01), but the difference was not statistically significant in the presence of other phylotypes. These data suggest that phylotype AP24 may play an important role in periodontal disease.     

Phenotypic and Molecular Biological Characterization of Cyanobacteria from Marble Surfaces of Treated and Untreated Sites of Propylaea (Acropolis,Athens)

Cyanobacteria cause aesthetic damage to marble surfaces and in particular their endolithic mode of life contributes to the breakdown of rock crystalline structures. The aim of this work was to estimate, with both phenotypical and molecular approach, the composition of cyanobacterial communities on the Propylaea marbles of the Acropolis Monuments. The two selected sampling sites were treated and untreated with a commercial biocide in order to estimate its effect on the cyanobacterial diversity. Our study revealed that in both sampling sites were present 13 phenotypes and 10 phylotypes and that the cyanobacterial taxa were considerably lower in the treated site.     

A quantitative study of calcareous stream and Tintenstriche algae from the Malham district,Northern England

The algal floras of two limestone streams and two calcareous Tintenstrichen are described and compared. The most important factor governing the distribution and abundance of species was the availability of water. Permanently wet stands, dominated by filamentous blue-green algae (Schizothrix calcicola and Phormidium incrustatum) had a greater species diversity than stands subject to frequent drying which were dominated by coccoid blue-green algae (Gloeocapsa spp.).

Significant correlations were found between S. calcicola and water pH (+ve), total species numbers and pH (+ve), filamentous blue-green algae and aufwuchs thickness (+ve) and Calothrix numbers and rock mass colonized (+ve).

The algal flora of the Tintenstrichen and the streams differed, although both developed upon the same limestone formation. The results are discussed with reference to previous work, substratum stability, aufwuchs structure, water chemistry, light and temperature.