Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community

The microbial community of a fermented molasses-fed sequencing batch reactor (SBR) operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was identified and quantified through a 16 S rRNA gene clone library and fluorescence in situ hybridization (FISH). The microbial enrichment was found to be composed of PHA-storing populations (84% of the microbial community), comprising members of the genera Azoarcus, Thauera and Paracoccus. The dominant PHA-storing populations ensured the high functional stability of the system (characterized by high PHA-storage efficiency, up to 60% PHA content). The fermented molasses contained primarily acetate, propionate, butyrate and valerate. The substrate preferences were determined by microautoradiography-FISH and differences in the substrate-uptake capabilities for the various probe-defined populations were found. The results showed that in the presence of multiple substrates, microbial populations specialized in different substrates were selected, thereby co-existing in the SBR by adapting to different niches. Azoarcus and Thauera, primarily consumed acetate and butyrate, respectively. Paracoccus consumed a broader range of substrates and had a higher cell-specific substrate uptake. The relative species composition and their substrate specialization were reflected in the substrate removal rates of different volatile fatty acids in the SBR reactor.     

A phylogenetic analysis of Pseudopaludicola (Anura) providing evidence of progressive chromosome reduction

Here, we present a molecular phylogenetic analysis of the Neotropical genus Pseudopaludicola focusing on species relationships including 11 of the 17 known species of Pseudopaludicola; several samples of Pseudopaludicola are not assigned to any species; and 34 terminal species as an outgroup. The study was based on the analysis of approximately 2.3 kb of the sequence of the mitochondrial 12S rRNA, tRNA^val and 16S rRNA genes through maximum parsimony and Bayesian phylogenetic reconstruction approaches. Our results showed that Pseudopaludicola is a well‐supported monophyletic group organized into four major clades and confirmed that the assemblage of species that lack T‐shaped terminal phalanges is paraphyletic with respect to the P. pusilla Group. Chromosomal data mapped on the cladogram showed a direct correlation among the four clades and observed chromosome numbers (2n = 22, 20, 18 and 16) with a progressive reduction in the chromosome number. Overall, our findings suggest that some taxonomic changes are necessary and reinforce the need for a revision of the genus Pseudopaludicola.     

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant–soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.     

Application of the direct beta counter Matrix 96 for cytotoxic assays: Simultaneous processing and reading of 96 wells using a51Cr-retention assay

To assess the cytotoxic activity of immune cells, we have developed a⁵¹Cr-retention assay in which the radioactivity retained by⁵¹Cr-labeled target cells, following coincubation with cytotoxic cells, is monitored using the automated Matrix 96 beta counter. The Matrix 96 is designed for simultaneously counting 96 samples isolated from a 96-well microplate. It uses 96 uniform and independent detectors operating on the principle of avalanche gas ionization in the Geiger-Muller mode. Samples must be dry because the detectors are of the open-window type. Therefore, samples from the 96 wells of the microplate are simultaneously harvested onto a filter using the MicroMate 196, a 96-well cell harvester, dried and quantified in the Matrix 96. Usually the⁵¹Cr isotope is measured by the detection of gamma radiation in gamma counters. The Matrix 96, however, monitors Auger electrons, which are also emitted by⁵¹Cr. We have shown that the retention assay can be used to monitor the cytotoxic activity of activated lymphocytes including lymphokine-activated killer cells and tumor-infiltrating lymphocytes against various tumor cell lines. This assay is most suitable for experiments in which low E/T ratios are sufficient to detect highly cytotoxic cells, such as clone screening in cloning assays or in limiting-dilution analysis assays. These assays involve processing and reading large numbers of microplates. In this case, the retention assay monitored in the Matrix 96 will improve the work flow and decrease the amount of radioactive waste.This work was supported by the American Cancer Society grant IN-162-C