The landscape of microbial phenotypic traits and associated genes

Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text. Moreover, the ProTraits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in metagenomes. Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability. A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. Our extended set of phenotype annotations allows detection of 57 088 high confidence gene-trait links, which recover many known associations involving sporulation, flagella, catalase activity, aerobicity, photosynthesis and other traits. Over 99% of the commonly occurring gene families are involved in genetic interactions conditional on at least one phenotype, suggesting that epistasis has a major role in shaping microbial gene content.     

Biosorption of phosphate from synthetic wastewater by biosolids

The aim of this study was to determine the potential of phosphate (P) removal from wastewater by biosolids prepared by the immobilization of P-accumulating bacteria onto organic bentonite. Organic bentonite was prepared by treating bentonite clay with quaternary ammonium salt — cetyltrimetylammonium (CTA) bromide. Cation exchange capacity (CEC) of the bentonite was found to be 179.0 meq/100 g of the dry bentonite. The CTA occupied ca. 175% of the CEC. Modification of bentonite with CTA in amounts higher than 55% of the CEC resulted in the change of zeta potential of particles from negative to positive. Only in reactors containing organic bentonite samples occupied with 3.5 and 28% of the CEC was P efficiently removed from wastewater by combined adsorption and bacterial uptake in the biomass. Organic bentonite samples with higher CTA loadings (from 55 to 175% of the CEC) showed bactericidal effects. To enhance P removal from wastewater in the aerated biological system, biosolids consisting of P-accumulating bacteria and organic bentonite can be used, but special attention should be given to the configuration of sorbed CTA molecules and its potential desorption.     

Genetic composition of the Jadro softmouth trout following translocation into a new habitat

Genetic founder effects of a historical translocation (1965; app. 12 generations ago) of endangered softmouth trout from the only remaining indigenous population to an adjacent uninhabited river were investigated. A comparison of 15 microsatellites from contemporary samples in both the source and re-established populations indicated a very low level of genetic diversity within the two populations. Furthermore, considerable differences in estimates of variability and effective population sizes were detected between populations, but no recent bottlenecks were evident. Our data suggest that the re-established population has lost variation due to genetic drift associated with founder effects following the translocation. Accordingly, in relation to management, we suggest that the re-established population could serve as a secondary source of individuals to buffer possible extinction due to demographic events. Finally, conservation initiatives to enhance the census population size and increase levels of variability in the re-established population are proposed. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Therapy effect of antiulcer agents on new chronic cysteamine colon lesion in rat

After demonstration that cysteamine induced duodenal lesions in gastrectomized rats, while a number of antiulcer drugs mitigated these lesions, it was shown that one single intrarectal (i.r.) cysteamine application produced severe colon lesions in acute studies in rats. Thus, the further focus was on the protracted effect of cysteamine challenge (400 mg/kg b.w. i.r.) and therapy influence in chronic experiments in female rats. Regularly, cysteamine colon lesions were markedly mitigated by ranitidine (10), omeprazole (10), atropine (10), methylprednisolone (1), sulphasalazine (50; mg/kg), pentadecapeptide BPC 157 (PL-10, PLD-116; 10 microg or 10 ng/kg). Specifically, after 1 or 3 months following initial challenge (cysteamine 400 mg/kg i.r.) in female rat, the therapy [BPC 157 (PL-10, PLD-116 (10.0 microg or 10.0 ng/kg; i.g., i.p., i.r.), ranitidine, omeprazole, atropine, methylprednisolone, sulphasalazine (i.p.)] reversed the protracted cysteamine colon injury: the 1 week-regimen (once daily application) started after 1 month post-cysteamine, as well as the 2 weeks-regimen (once daily application), which started after 3 months. The effect on recidive lesion was also tested. These cysteamine lesions may reappear after stopping therapy (after stopping therapy for 3 weeks at the end of 2-weeks regimen started in 3 months-cysteamine female rats) in sulphasalazine group, while this reappearance is markedly antagonized in pentadecapeptide BPC 157 (PL-10, PLD-116)-rats (cysteamine-colon lesion still substantially low).