Specific Detection and Real-Time PCR Quantification of Potentially Mycophagous Bacteria Belonging to the Genus Collimonas in Different Soil Ecosystems

The bacterial genus Collimonas has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. Here, we report the first field inventory of the occurrence and abundance of Collimonas in soils (n = 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of Collimonas and fungal biomass. Estimates of fungal densities were based on ergosterol measurements. Each soil was also characterized in terms of its physical and chemical properties and vegetation and management types. Culturable Collimonas was identified in plate-spread soil samples by its ability to clear colloidal chitin, in combination with a Collimonas-specific restriction fragment length polymorphism analysis of 16S rRNA PCR amplified from individual colonies. Using this approach, we found culturable collimonads only in (semi)natural grasslands. A real-time PCR assay for the specific quantification of Collimonas 16S rRNA in total soil DNA was developed. Collimonas was detectable in 80% of the soil samples, with densities up to 10⁵ cells g⁻¹ (dry weight) soil. The numbers of Collimonas cells per gram of soil were consistently lowest in fungus-poor arable soils and, surprisingly, also in fungus-rich organic layers of forest soils. When all soils were included, no significant correlation was observed between the number of Collimonas cells and ergosterol-based soil fungal biomass. Based on this result, we rejected our null hypothesis, and possible explanations for this were addressed.     

Identification of Multiple Protective Epitopes (Protectopes) in the Central Conserved Domain of a Prototype Human Respiratory Syncytial Virus G Protein

A recombinant fusion protein (BBG2Na) comprising the central conserved domain of the respiratory syncytial virus subgroup A (RSV-A) (Long) G protein (residues 130 to 230) and an albumin binding domain of streptococcal protein G was shown previously to protect mouse upper (URT) and lower (LRT) respiratory tracts against intranasal RSV challenge (U. F. Power, H. Plotnicky-Gilquin, T. Huss, A. Robert, M. Trudel, S. Stahl, M. Uhlén, T. N. Nguyen, and H. Binz, Virology 230:155-166, 1997). Panels of monoclonal antibodies (MAbs) and synthetic peptides were generated to facilitate dissection of the structural elements of this domain implicated in protective efficacy. All MAbs recognized native RSV-A antigens, and five linear B-cell epitopes were identified; these mapped to residues 152 to 163, 165 to 172, 171 to 187 (two overlapping epitopes), and 196 to 204, thereby covering the highly conserved cysteine noose domain. Antibody passive-transfer and peptide immunization studies revealed that all epitopes were implicated in protection of the LRT, but not likely the URT, against RSV-A challenge. Pepscan analyses of anti-RSV-A and anti-BBG2Na murine polyclonal sera revealed lower-level epitope usage within the central conserved region in the former, suggesting diminished immunogenicity of the implicated epitopes in the context of the whole virus. However, Pepscan analyses of RSV-seropositive human sera revealed that all of the murine B-cell protective epitopes (protectopes) that mapped to the central conserved domain were recognized in man. Should these murine protectopes also be implicated in human LRT protection, their clustering around the highly conserved cysteine noose region will have important implications for the development of RSV vaccines.     

Brucella suis histidinol dehydrogenase: synthesis and inhibition studies of substituted N-L-histidinylphenylsulfonyl hydrazide

Histidinol dehydrogenase (HDH, EC EC1.1.1.23) catalyses the final step in the biosynthesis of histidine and constitutes an attractive novel target for the development of new agents against the pathogenous, bacteria Brucella suis. A small library of new HDH inhibitors based on the L-histidinylphenylsulfonyl hydrazide scaffold has been synthesized and their inhibitory activity investigated. The obtained results demonstrate that modification of the group between the histidinyl moiety and the phenyl ring constitutes an important structural factor for the design of effective HDH inhibitors.     

Identification of Brevibacteriaceae by Multilocus Sequence Typing and Comparative Genomic Hybridization Analyses

Multilocus sequence typing with nine selected genes is shown to be a promising new tool for accurate identifications of Brevibacteriaceae at the species level. A developed microarray also allows intraspecific diversity investigations of Brevibacterium aurantiacum showing that 13% to 15% of the genes of strain ATCC 9174 were absent or divergent in strain BL2 or ATCC 9175.Brevibacteriaceae play a major part in the cheese smear community (6, 11). The classification and typing of cheese-related Brevibacteriaceae have been based mainly on molecular methods such as amplified ribosomal DNA restriction enzyme analysis, pulsed-field gel electrophoresis, and ribotyping (8, 10, 12). Recently, the original Brevibacterium linens group was split into two species on the basis of their physiological and biochemical characteristics, the sugar and polyol composition of their teichoic acids, and their 16S rRNA sequence and DNA-DNA hybridization levels. One species remains B. linens and is represented by type strain ATCC 9172. The other, represented by type strain ATCC 9175, has been renamed Brevibacterium aurantiacum. Regarding this new classification, the taxonomic position of cheese-related isolates has to be revisited and potential relationships between phylogenetic affiliation and the potential occurrence of given metabolic characteristics redefined (7). The unfinished genome sequence of B. aurantiacum ATCC 9174 has recently been released by the Joint Genome Institute (http://genome.jgi-psf.org/draft_microbes/breli/breli.home.html). The development of focused phylogenetic approaches using multiple markers in conjunction with whole-genome screening techniques such as comparative genomic hybridization (CGH) has proven to be useful for the detailed characterization of pathogenic species, including food pathogens (3, 5, 9). However, only a few technological species have been investigated at an intraspecies level (2). Our intention was thus to develop modern tools to facilitate the typing of strains of technological interest, for which Brevibacteriaceae could be used as a case study.     

Marsh management, reserve creation, hunting periods and carrying capacity for wintering ducks and coots

Many wild species, like waterbirds, are exploited for their economic interests. At present, the annual western Palearctic duck bag is at least 17 million birds. From a sustainable management perspective, wetland users and managers request predictions of spatial distribution and abundance variations of these bird populations. The objective of this study was to analyze local factors potentially influencing the diurnal distribution and population size of wintering ducks and coots, the main game species, in Camargue (southern France). First, we showed that marshland surface area, salinity and hunting disturbance were the principal variables explaining the duck and coot distribution. Secondly, we tested the hypothesis that hunting disturbance would reduce the carrying capacity of the Camargue with two analyses: the effect of creating a protected area and the change of the hunting closing date. This hypothesis was not validated. Our study therefore led us to reconsider the research orientations on the carrying capacity in this wetland. The surface of protected day roosts seems presently sufficient in the Rhone delta. Consequently, to increase the population size with the same level of hunting disturbance at the scale of the Camargue, alternative strategies should be envisaged, such as the creation of nature reserves on nocturnal feeding ground or the creation of large management units with limited disturbance.     

Carbonic anhydrase inhibitors. Inhibition of the fungal β-carbonic anhydrases from Candida albicans and Cryptococcus neoformans with boronic acids

Inhibition of the β-carbonic anhydrases (CAs, EC 4.2.1.1) from the pathogenic fungi Cryptococcus neoformans (Can2) and Candida albicans (Nce103) with a series of aromatic, arylalkenyl- and arylalkylboronic acids was investigated. Aromatic, 4-phenylsubstituted- and 2-naphthylboronic acids were the best Can2 inhibitors, with inhibition constants in the range of 8.5–11.5 μM, whereas arylalkenyl and aryalkylboronic acids showed K_Is in the range of 428–3040 μM. Nce103 showed a similar inhibition profile, with the 4-phenylsubstituted- and 2-naphthylboronic acids possessing K_Is in the range of 7.8–42.3 μM, whereas the arylalkenyl and aryalkylboronic acids were weaker inhibitors (K_Is of 412–5210 μM). The host human enzymes CA I and II were also effectively inhibited by these boronic acids. The B(OH)₂ moiety is thus a new zinc-binding group for designing effective inhibitors of the α- and β-CAs.     

Impact of Collimonas bacteria on community composition of soil fungi

The genus Collimonas consists of soil bacteria that have the potential to grow at the expense of living fungal hyphae. However, the consequences of this mycophagous ability for soil fungi are unknown. Here we report on the development of fungal communities after introduction of collimonads in a soil that had a low abundance of indigenous collimonads. Development of fungal communities was stimulated by addition of cellulose or by introducing plants ( Plantago lanceolata ). Community composition of total fungi in soil and rhizosphere and of arbuscular mycorrhizal fungi in roots was examined by PCR-DGGE. The introduction of collimonads altered the composition of all fungal communities studied but had no effects on fungal biomass increase, cellulose degrading activity or plant performance. The most likely explanation for these results is that differences in sensitivity of fungal species to the presence of collimonads result in competitive replacement of species. The lab and greenhouse experiments were complemented with a field experiment. Mesh bags containing sterile sand with or without collimonads were buried in an ex-arable field and a forest. The presence of collimonads had an effect on the composition of fungi invading these bags in the ex-arable site but not in the forest site.