Controlled binding of liposomes to cultured cells by means of lectins

Lectin-mediated binding of liposomes to Hela cells was analyzed as a function of different parameters. We show that the amount of lectin covalently bound to liposomes can be accurately controlled. We chose to work with 500 - to 1 000 molecules of WGA bound per liposome of 1 micron diameter. These liposomes bound very efficiently to Hela cells as demonstrated by fluorescent microscopy, and fluorescent cell-sorting. We show that the number of liposomes bound is proportional to the input, over a wide range of concentrations. The liposomes bound very tightly to cells and could not be removed by trypsin or N-acetylglucosamine, which competes with WGA binding.     

Comparative Genetic Diversity of the narG, nosZ, and 16S rRNA Genes in Fluorescent Pseudomonads

The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overall, there was a good correspondence between the reductase activities and the presence of the corresponding genes. Distribution in the different ribotypes of strains harboring both the narG and nosZ genes and of strains missing both genes suggests that these two groups of strains had different evolutionary histories. Both dissimilatory genes showed high polymorphism, with similarity indexes (Jaccard) of between 0.04 and 0.8, whereas those of the 16S rRNA gene only varied from 0.77 to 0.99. No correlation between the similarity indexes of 16S rRNA and dissimilatory genes was seen, suggesting that the evolution rates of ribosomal and functional genes differ. Pairwise comparison of similarity indexes of the narG and nosZ genes led to the delineation of two types of strains. Within the first type, the similarity indexes of both genes varied in the same range, suggesting that these two genes have followed a similar evolution. Within the second type of strain, the range of variations was higher for the nosZ than for the narG gene, suggesting that these genes have had a different evolutionary rate.     

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers.     

Olfactory impairment is correlated with confabulation in alcoholism: towards a multimodal testing of orbitofrontal cortex

Background

Olfactory abilities are now a flourishing field in psychiatry research. As the orbitofrontal cortex appears to be simultaneously implicated in odour processing and executive impairments, it has been proposed that olfaction could constitute a cognitive marker of psychiatric states. While this assumption appears promising, very few studies have been conducted on this topic among psychopathological populations. The present study thus aimed at exploring the links between olfaction and executive functions. These links were evaluated using two tasks of comparable difficulty, one known to rely on orbitofrontal cortex processing (i.e., a confabulation task), and one not associated with this area (i.e., Stop-Signal task).

Methodology/Principal Findings

Twenty recently detoxified alcoholic individuals and twenty paired controls took part in an experiment evaluating olfactory abilities and executive functioning (i.e., Stop-Signal task and confabulation task). Comorbidities and potential biasing variables were also controlled for. Alcoholic individuals exhibited impaired performance for high-level olfactory processing and significant confabulation problems as compared to controls (but no deficit in Stop-Signal task), even when the influence of comorbidities was taken into account. Most importantly, olfactory abilities and confabulation rates were significantly correlated in both groups.

Conclusions/Significance

Alcoholism jointly leads to olfactory and memory source impairments, and these two categories of deficits are associated. These results strongly support the proposition that olfactory and confabulation measures both index orbitofrontal functioning, and suggest that olfaction could become a reliable cognitive marker in psychiatric disorders. Moreover, it underlines the need to take into account these olfactory and source memory impairments in a clinical context.     

The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

Nitrous oxide (N₂O) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to nitrogen gas (N₂) by bacteria and archaea harboring the N₂O reductase (N₂OR), which is the only known N₂O sink in the biosphere. Despite its crucial role in mitigating N₂O emissions, knowledge of the N₂OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N₂OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N₂O-reducing communities. Examination of N₂OR structural elements not considered in the phylogeny revealed that the two clades differ in their signal peptides, indicating differences in the translocation pathway of the N₂OR across the membrane. Sequencing of environmental clones of the previously undetected nosZ lineage in various environments showed that it is widespread and diverse. Using quantitative PCR, we demonstrate that this clade was most often at least as abundant as the other, thereby more than doubling the known extent of the overall N₂O-reducing community in the environment. Furthermore, we observed that the relative abundance of nosZ from either clade varied among habitat types and environmental conditions. Our results indicate a physiological dichotomy in the diversity of N₂O-reducing microorganisms, which might be of importance for understanding the relationship between the diversity of N₂O-reducing microorganisms and N₂O reduction in different ecosystems.     

Extreme 15N-enrichments in 2.72-Gyr-old sediments: evidence for a turning point in the nitrogen cycle

Although nitrogen is a key element in organic molecules such as nucleic acids and proteins, the timing of the emergence of its modern biogeochemical cycle is poorly known. Recent studies on the antiquity of the nitrogen cycle and its interaction with free oxygen suggests the establishment of a complete aerobic N biogeochemical cycle with nitrification, denitrification, and nitrogen fixation at about 2.68 Gyr. Here, we report new bulk nitrogen isotope data for the 2.72 billion-year-old sedimentary succession of the Tumbiana Formation (Pilbara Craton, Western Australia). The nitrogen isotopic compositions vary widely from +8.6‰ up to +50.4‰ and are inversely correlated with the very low δ(13)C values of associated organic matter defining the Fortescue excursion (down to about -56‰). We propose that this (15)N-enrichment records the onset of nitrification coupled to the continuous removal of its derivatives (nitrite and nitrate) by denitrification. This finding implies an increase in the availability of electron acceptors and probably oxygen in the Tumbiana depositional environment, 300 million years before the oxygenation of the Earth's atmosphere.     

Towards food, feed and energy crops mitigating climate change

Agriculture is an important source of anthropogenic emissions of the greenhouse gases (GHG), methane (CH(4)) and nitrous oxide (N(2)O), and crops can affect the microbial processes controlling these emissions in many ways. Here, we summarize the current knowledge of plant-microbe interactions in relation to the CH(4) and N(2)O budgets and show how this is promoting new generations of crop cultivars that have the potential to mitigate GHG emissions for future agricultural use. The possibility of breeding low GHG-emitting cultivars is a paradigm shift towards sustainable agriculture that balances climate change and food and bioenergy security.     

Sulfur isotope's signal of nanopyrites enclosed in 2.7 Ga stromatolitic organic remains reveal microbial sulfate reduction

Microbial sulfate reduction (MSR) is thought to have operated very early on Earth and is often invoked to explain the occurrence of sedimentary sulfides in the rock record. Sedimentary sulfides can also form from sulfides produced abiotically during late diagenesis or metamorphism. As both biotic and abiotic processes contribute to the bulk of sedimentary sulfides, tracing back the original microbial signature from the earliest Earth record is challenging. We present in situ sulfur isotope data from nanopyrites occurring in carbonaceous remains lining the domical shape of stromatolite knobs of the 2.7‐Gyr‐old Tumbiana Formation (Western Australia). The analyzed nanopyrites show a large range of δ³⁴S values of about 84‰ (from ?33.7‰ to +50.4‰). The recognition that a large δ³⁴S range of 80‰ is found in individual carbonaceous‐rich layers support the interpretation that the nanopyrites were formed in microbial mats through MSR by a Rayleigh distillation process during early diagenesis. An active microbial cycling of sulfur during formation of the stromatolite may have facilitated the mixing of different sulfur pools (atmospheric and hydrothermal) and explain the weak mass independent signature (MIF‐S) recorded in the Tumbiana Formation. These results confirm that MSR participated actively to the biogeochemical cycling of sulfur during the Neoarchean and support previous models suggesting anaerobic oxidation of methane using sulfate in the Tumbiana environment.     

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.Subject terms: Soil microbiology, Ecology