Characteristics of human intestinal Escherichia coli with changing environments

To investigate if the characteristics of human intestinal Escherichia coli are changing with the environment of the host, we studied intestinal E. coli from subjects having recently migrated from a temperate to a tropical area. We determined the phylogenetic group, the prevalence of the antibiotic resistance, the presence of integrons and the strain diversity in faecal isolates from 25 subjects originally from metropolitan France and expatriated to French Guyana. These characteristics were compared with those of 25 previously studied Wayampi Amerindian natives of French Guyana and from 25 metropolitan French residents. The three groups of subjects were matched for age and sex, had not taken antibiotics for at least 1 month, nor had been hospitalized within the past year. In all, the characteristics of intestinal E. coli from Expatriates were intermediate between those found in residents from metropolitan France and those found in natives of French Guyana. Prevalence of carriage of resistant Gram-negative bacteria in Expatriates was intermediate between French residents and Wayampi as were the prevalence of integrons in E. coli (12.3% versus 16.3% and 7.8% respectively), and the intra-host diversity of E. coli (2.3 strains/subject versus 1.9 and 3.1, respectively); lastly, in Expatriates, the prevalence of carriage of phylogenetic group B2 strains was lower than in French residents (16% versus 56%, P  = 0.005), while carriage of phylogenetic group A strains was lower than in Wayampi (56% versus 88%, P  = 0.03). Our results suggest that the composition of the commensal intestinal flora of humans is not static but changes dynamically in response to new environmental conditions.     

Microorganisms of the San Francisco Sour Dough Bread Process: I. Yeasts Responsible for the Leavening Action

Two hundred isolates from San Francisco sour dough French bread fermentations (40 from each of five different bakeries) were screened by fermentation tests and for their ability to grow in the presence of cycloheximide (Actidione). All of the isolates from four of the bakeries and 70% of those from the fifth were unable to utilize maltose but grew well on other sugars, even in the presence of cycloheximide. The remaining few isolates from the fifth bakery utilized maltose but not galactose and were inhibited by cycloheximide. No bakers' yeast types were found. Sixteen of the maltose-negative and five of the galactose-negative isolates were subjected to more rigorous taxonomic procedures. All of the maltose-negative isolates were identified as asporogenous strains of Saccharomyces exiguus (Torulopsis holmii) and the galactose-negative ones, as S. inusitatus. The predominance of S. exiguus, its vigor in the particular acidic environment of the sour dough, and the correlation of its numbers with the leavening function constitute strong evidence on the role of this organism in the sour dough system.     

Diversity of Rock-Inhabiting Cyanobacterial Lichens: Studies on Granite Inselbergs along the Orinoco and in Guyana

Abstract: A survey was undertaken of specialized saxicolous cyanobacterial lichens growing on exposed granitic rock surfaces of inselbergs in Venezuela and additionally in Guyana and French Guyana. The study focused on taxonomy and species composition. Twenty-three cyanobacterial lichens were found, four of which are new to science: Peltula auriculata, Phylliscum vermiformis, Psorotichia polyspora and Pterygiopsis guyanensis. Besides the new species, almost all taxa are absent from the available lists of lichen-forming fungi from the Guyana region. Although free-living cyanobacteria are the dominant group in biological crusts covering the inselbergs, the number of cyanobacterial lichens is relatively high and their distribution is homogenous over long distances and macro-climatic gradients. As inselberg rock faces undergo relatively fast weathering under moist tropical climates, numerous micro-habitats are formed. Among these, xeric micro-habitats are favourable for colonization by cyanobacterial lichens, mainly of the Lichinaceae and Peltulaceae. It is concluded that granite inselbergs in the savannas of the Orinoco lowland and the Guyana region are local centres of diversity for saxicolous cyanobacterial lichens.     

Humicolous buthoid scorpions: a new genus and species from French Guiana

A new genus and species of humicolous buthid scorpion are described on the basis of a single specimen collected in French Guyana. New considerations on the taxonomy and morphology of some micro-buthoid humicolous scorpions are proposed, mainly based on the study by scanning electron microscopy of the peg-shaped sensillae of the pectines.     

Cetobacterium somerae sp. nov. from human feces and emended description of the genus Cetobacterium

Phenorypic and phylogenetic studies were performed on four isolates of an unidentified gram-negative, microaerotolerant, non-spore-forming, rod-shaped bacterium isolated from the feces of children. The unknown organism was bile resistant and produced acetic acid as the major end product of metabolism of peptides and carbohydrates. It possessed a low DNA G + C content of 31 mol %. Comparative 16S rRNA gene sequencing demonstrated that the four isolates were phylogenetically identical (100% 16S rRNA sequence similarity) and represent a hitherto unknown sub-line within the genus Cetobacterium. The novel bacterium displayed approximately 5% sequence divergence with Cetobacterium ceti, and can be readily distinguished from the latter by physiological and biochemical criteria. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown fecal bacterium be classified in the genus Cetobacterium, as Cetobacterium somerae sp. nov. The proposed type strain of Cetobacterium somerae is WAL 14325(T) (ATCC BAA-474(T) = CCUG 46254T).     

Pathogenic Variability in Mycosphaerella brassicicola, the Causal Agent of the Ringspot Disease of Crucifers

Twenty monoascosporic isolates of Mycosphaerella brassicicola from diverse origins were inoculated to 13 different accessions of cauliflower. No hypersensitive response was noticed and the isolates exhibited variable pathogenicity. Three isolates from cauliflower were isolated from the same lesion and had variable pathogenicity. This result suggests that different infection units e.g. ascospores contribute to the development of a single lesion. Furthermore, this finding also indicates that one should work with monoascosporic isolates. Pathogenicity results of this study showed that European isolates from cabbages had reduced pathogenicity compared to French cauliflower ones. Variable levels of pathogenicity were found in French cauliflower isolates. This group had also the most aggressive isolates. Our results suggest that Brittany may be a diversification area for the pathogen. In fact, the climate is mild and humid and crucifers (e.g. cauliflower and broccoli) are continuously grown over the year in this region. Pathotypes found in other growing areas may have moved from Brittany. All these findings supported by other studies suggest that resistance sources available in other countries may not be effective in Brittany. Consequently, screening for resistance sources should be done with cauliflower isolates from Brittany. No accession tested was susceptible or resistant to all isolates tested.     

New species of Hypocreales (Fungi,Ascomycetes)

The new ascomycetes Hypomyces succineus, Podostroma eperuae, and Nectria phialotrichi are proposed. Hypomyces succineus occurs on basidiomata of Pholiota sp. in New York; its anamorph is described as the new species Cladobotryum succineum. Podostroma eperuae occurs on decaying pods of a species of Eperua found in French Guiana and Guyana. Its anamorph is unknown. Nectria phialotrichi occurs on perithecia of Nectria sp. and bark in Guyana; its anamorph is referred to the anamorph genus Onychophora.     

Antagonistic and plant growth promoting activities of endophytic and soil actinomycetes

The objective of this study was the isolation and screening of actinomycete isolates for antagonistic potential and plant growth promoting activities. A total of 321 isolates were recovered from different plants, their rhizospheric soils and non-rhizospheric soils of Punjab and Himachal Pradesh regions. Out of these, 62 were endophytic, 156 were rhizospheric and 103 were non-rhizospheric isolates. In primary screening (dual culture assay), 83 isolates antagonised one or more test phytopathogenic fungi. From these active isolates, 20 were found to be antagonistic in well diffusion assay (secondary screening) and most of them demonstrated broad spectrum inhibitory activity against five to six test fungi. Studies on plant growth promoting activities revealed that 12 showed abilities to produce indole acetic acid, 10 produced siderophores and 12 showed ammonia production. Phosphate solubilisation was observed in five isolates and four fixed atmospheric N₂. In addition, production of hydrolytic enzymes such as chitinase, amylase, cellulase and protease was demonstrated by five, twenty, eleven and eleven isolates, respectively. The results of this study indicate that these isolates may be used as biocontrol and plant growth promoting agents. Morphological and chemotaxonomic studies revealed that all the active isolates belonged to the genus Streptomyces     

Patterns of coral-dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host-symbiont selectivity

Like other reef-building corals, members of the genus Acropora form obligate endosymbioses with dinoflagellates (zooxanthellae) belonging to the genus Symbiodinium. Both Symbiodinium and its hosts are diverse assemblages, and the relationships between host and algal genotypes are unclear. In this study, we determined phylogenetic relationships between Symbiodinium isolates from a wide range of Acropora species and plotted the algal genotypes onto a molecular phylogeny of 28 Acropora species, using the same samples for the host and symbiont genotyping. In addition, we performed a preliminary survey of zooxanthella distribution in Acropora species from the central Great Barrier Reef. Three of the four known major zooxanthellae clades were represented in the 168 samples examined, and within the major clade C, three distinct subclades were identified. No evidence was found for coevolution, but several clear patterns of specificity were identified. Moreover, composition of the zooxanthella pool varied among locales and in one host species we found light-related patterns of zooxanthella distribution.     

Filamentous fungi found in Atta sexdens rubropilosa colonies after treatment with different toxic bait formulations

Leaf‐cutting ants maintain a symbiotic relationship with basidiomycetous fungi cultivated as food. Here, we profiled the non‐symbiotic filamentous fungi in laboratory nests of Atta sexdens rubropilosa submitted to treatments with different toxic bait formulations (using the insecticide sulfluramide as the active ingredient). After treatment, several filamentous fungi were found in different nest compartments. Culture‐dependent techniques recovered a total of 93 fungal isolates comprising 10 genera, 11 species and four unidentified fungi. The genus Penicillium was prevalent in both control and insecticide treatments. Overall, the majority of fungal isolates obtained in this study are commonly found in soil. Escovopsis spp., the specialized parasite of the ant‐fungus mutualism was only recorded in the fungus gardens of nests submitted to the toxic treatments. Moreover, no correlation was found regarding the presence of fungi in the different nest compartments (chi‐square, P > 0.4182). This study reveals that Escovopsis spp. is not the only fungus to overgrow the fungus garden of debilitated nests, thus adding more evidence on the possible negative impacts of such alien fungi. As suggested by previous studies, fast‐growing filamentous fungi likely overgrow the fungus garden in such conditions.     

Low degree of human T-cell leukemia/lymphoma virus type I genetic drift in vivo as a means of monitoring viral transmission and movement of ancient human populations.

We have studied the genetic variation of human T-cell leukemia/lymphoma virus type I (HTLV-I) isolates in the same individuals over time, as well as of HTLV-I isolates from various parts of the world. The viral DNA fragment studied encodes the carboxy terminus of gp46 and almost all of gp21, both of which are envelope glycoproteins. Samples were obtained from native inhabitants of five African countries, two South American countries, China, the French West Indies, and Haiti and included 14 patients with tropical spastic paraparesis/HTLV-I-associated myelopathy, 10 patients with adult T-cell leukemia, 1 patient with T-cell non-Hodgkin's lymphoma, and 3 healthy HTLV-I-seropositive individuals. DNA analyses of HTLV-I sequences demonstrated that (i) little or no genetic variation occurred in vivo in the same individual or in different hosts from the same region carrying the same virus, regardless of their clinical statuses; (ii) changes in nucleotide sequences in some regions of the HTLV-I genome were diagnostic of the geographical origin of the viruses; (iii) HTLV-I sequences from West African countries (Mauritania and Guinea Bissau) and some from the Ivory Coast and Central African Republic were virtually identical to those from the French West Indies, Haiti, French Guyana, and Peru, strongly suggesting that at least some HTLV-I strains were introduced into the New World through infected individuals during the slave trade events; and (iv) the Zairian HTLV-I isolates represent a separate HTLV-I cluster, in which intrastrain variability was also observed, and are more divergent from the other HTLV-I isolates. Because of the low genetic variability of HTLV-I in vivo, the study of the proviral DNA sequence in selected populations of infected individuals will increase our knowledge of the origin and evolution of HTLV-I and might be useful in anthropological studies.     

Anamorphic fungi from French Guyana: two undescribed Gliocephalotrichum species (Nectriaceae, Hypocreales)

Morphological and molecular studies of Gliocephalotrichum collections from rain forest leaf litter in French Guyana revealed the occurrence of two undescribed species, described here as G. bacillisporum and G. longibrachium. Both species have a whorl of sterile stipe extensions directly subtending the conidiogenous penicilli. Gliocephalotrichum bulbilium also was isolated from leaf litter in French Guyana. Two sequences in GenBank, of uncultured ascomycetes from Gabon, Africa, cluster in the Gliocephalotrichum clade, suggesting the probable existence of additional undescribed taxa from the Central African rainforest.     

Unraveling the extent of diversity within the order Planctomycetales.

The phylogenetic positions of 22 isolates that morphologically resemble members of the family Planctomycetaceae were determined by sequence analysis of genes coding for 16S rRNA. While nine and eight isolates could be assigned to the genera Planctomyces and Pirellula, respectively, three strains grouped near Isosphaera pallida and one strain was closely related to Gemmata obscuriglobus. No isolate was found to be related to a previously described species of any of the four genera at the species level. Morphological characters and sequence idiosyncrasies of genes coding for 16S rRNA of the isolates generally correlated with features described for the four genera to which the isolates could be assigned. One strain stands phylogenetically isolated and may be representative of a novel genus of the family. Comparison with environmental clone sequences representing planctomycetes in soil and water revealed that three of the novel isolates were related to one clone of soil origin, but no close relationships between clones and the other new strains were found. The study reveals that the biodiversity of planctomycetes is significantly greater than was previously determined.     

Identification of nitrogen-fixing Paenibacillus from different plant rhizospheres and a novel nifH gene detected in the P. stellifer

A total of 534 isolates were selectively obtained from different plant rhizospheres based on their growth on nitrogen-free medium and their resistance to 80 degrees C for 15 min. Of the 534 isolates, 23 isolates had nifH gene and exhibited nitrogenase activities. Based on 16S rDNA sequence, G + C content assay and DNA-DNA hybridization, by the 23 isolates, which were divided into four monophyletic clusters, all belonged to the Paenibacillus genus. NifH gene deduced amino acid alignment analysis revealed that cluster I, including 15 isolates, showed the highest NifH identity with Paenibacillus genus; while cluster II identified as P stellifer by DNA-DNA hybridization was consistent with four uncultured bacterial clones. This study suggested that the nitrogen-fixing Paenibacillus were distributed in various ecosystems and prevalent in different plant rhizospheres. It was the first demonstration that nitrogen fixation existed in P. jamilae and P. stellifer. In eight isolates identified as P. stellfer species, a novel nifH gene was detected in Paenibacillus.     

The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae.

The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth- or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventh-pandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.     

A new peronosporomycete, <Emphasis Type="Italic">Halioticida noduliformans</Emphasis> gen. et sp. nov., isolated from white nodules in the abalone <Emphasis Type="Italic">Haliotis</Emphasis> spp. from Japan

Four strains belonging to the Peronosporomycetes (formerly Oomycetes) were isolated from white nodules found on the mantle of three species of abalone. In artificial seawater, the four isolates formed fragments such as in the genus Haliphthoros, but the protoplasm constriction was weaker, and fragments were longer, with smaller spaces between them, than those of Haliphthoros. The four strains form one or more discharge tubes from each zoosporangium. The four strains were similar, but not identical, to the genus Haliphthoros based on morphological characteristics. As a result, the four isolates were classified in a new genus and species, Halioticida noduliformans gen. et sp. nov. Phylogenetic analysis of the D1/D2 region of the large subunit ribosomal RNA gene (LSU rDNA) was performed, and the four isolates showed 100%–99.8% concordance. In the phylogenetic tree, the four isolates were not classified in the subclass Peronosporomycetidae, Saprolegniomycetidae, or Rhipidiomycetidae. However, the four isolates formed a new clade with genera Haliphthoros and Halocrusticida in Peronosporomycetes. Within this new clade, the four isolates, Haliphthoros spp. and Halocrusticida spp., were grouped in their respective independent subclades. These results showed that these were the new genus and species from the morphological characteristics.     

Phylogenetic analysis of Cryptosporidium parasites based on the small-subunit rRNA gene locus

Biological data support the hypothesis that there are multiple species in the genus Cryptosporidium, but a recent analysis of the available genetic data suggested that there is insufficient evidence for species differentiation. In order to resolve the controversy in the taxonomy of this parasite genus, we characterized the small-subunit rRNA genes of Cryptosporidium parvum, Cryptosporidium baileyi, Cryptosporidium muris, and Cryptosporidium serpentis and performed a phylogenetic analysis of the genus Cryptosporidium. Our study revealed that the genus Cryptosporidium contains the phylogenetically distinct species C. parvum, C. muris, C. baileyi, and C. serpentis, which is consistent with the biological characteristics and host specificity data. The Cryptosporidium species formed two clades, with C. parvum and C. baileyi belonging to one clade and C. muris and C. serpentis belonging to the other clade. Within C. parvum, human genotype isolates and guinea pig isolates (known as Cryptosporidium wrairi) each differed from bovine genotype isolates by the nucleotide sequence in four regions. A C. muris isolate from cattle was also different from parasites isolated from a rock hyrax and a Bactrian camel. Minor differences were also detected between C. serpentis isolates from snakes and lizards. Based on the genetic information, a species- and strain-specific PCR-restriction fragment length polymorphism diagnostic tool was developed.     

Specific epithets of the flowering plants of central French Guiana

The epithets of the flowering plants of central French Guiana are classified into derivation categories. Specific epithets of the flowering plants of central French Guiana refer mostly to shapes (274 species), persons (252), places (212), appearance (146), and size (140). These categories account for 55% of names given to the plants of this flora. The most prolific publishers of names for the flora of central French Guiana are Aublet and Linnaeus, who were respectively the authors of 177 and 110 of the names of species (15% of the total) found in the flora of central French Guiana. Although many of the species names, such as those relating to place and person, are easy to categorize, many others are open to different interpretations. Specific epithets with different orthographies derived from Guiana or Guyana are discussed. In addition, problems in the use of diacritical marks and inconsistencies with spacing between the abbreviations of given names and surnames of authors of plant names are noted.     

Potentially Pathogenic Acanthamoeba Isolated from a Hospital in Brazil

Studies on free-living amoebae (FLA), has been increased in recent years, especially related to the genus Acanthamoeba, because these organisms are widely found in the environment. The present work isolated and characterized this organism from biofilms and dust in hospital environment. 135 samples were collected in 15 different environments in a hospital at the south of Brazil. Thirty-one (23%) isolates were identified as morphologically belonging to the Acanthamoeba genus and 10 of these were submitted to temperature and osmotolerance tests as criterion for evaluation of the viability and pathogenicity. The tests indicate that four (40%) of these isolates could be potentially pathogenic because grew at high temperature (40°C) and osmolarity (mannitol 1 M). Some isolates genotypes were determined after ribosomal DNA sequencing. These data revealed that three dust isolates belong to T4, two biofilm isolates to T5 and one dust isolate to T3 genotype. Therefore, Acanthamoeba found in the hospital environment represents a risk for people that circulate there.