Construction and preliminary analysis of a metagenomic library from a deep-sea sediment of east Pacific Nodule Province

The Pacific Nodule Province is a unique ocean area containing an abundance of polymetallic nodules. To explore more genetic information and discover potentially industrial useful genes of the microbial community from this particular area, a cosmid library with an average insert of about 35 kb was constructed from the deep-sea sediment. The bacteria in the cosmid library were composed mainly of Proteobacteria including Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. The end sequences of some cosmid clones were determined and the complete insert sequences of two cosmid clones, 10D02 and 17H9, are presented. 10D02 has a length of 40.8 kb and contains 40 predicted encoding genes. It contains a partial 16S rRNA gene of Alphaproteobacteria. 17H9 is 36.8 kb and predicted to have 31 encoding genes and a 16S-23S-5S rRNA gene operon. Phylogenetic analysis of 16S and 23S rRNA gene sequence on the 17H9 both reveals that the inserted DNA from 17H9 came from a novel Alphaproteobacteria and is closely related to Magnetospirillum species. The predicted proteins of ORF 1-11 also have high identity to those of Magnetospirillum species, and the organization of these genes is highly conserved among known Magnetospirillum species. The data suggest that the retrieved DNA in 17H9 might be derived from a novel Magnetospirillum species.     

Arbuscular mycorrhizal symbiosis can counterbalance the negative influence of the exotic tree species Eucalyptus camaldulensis on the structure and functioning of soil microbial communities in a sahelian soil

The hypothesis of the present study was that bacterial communities would differentiate under Eucalyptus camaldulensis and that an enhancement of arbuscular mycorrhizal (AM) density would minimize this exotic plant species effect. Treatments consisted of control plants, preplanting fertilizer application and AM inoculation. After 4 months of culture in autoclaved soil, E. camaldulensis seedlings were either harvested for growth measurement or transferred into containers filled with the same soil but not sterilized. Other containers were kept without E. camaldulensis seedlings. After 12 months, effects of fertilizer amendment and AM inoculation were measured on the growth of Eucalyptus seedlings and on soil microbial communities. The results clearly show that this plant species significantly modified the soil bacterial community. Both community structure (assessed by denaturing gradient gel electrophoresis profiles) and function (assessed by substrate-induced respiration responses including soil catabolic evenness) were significantly affected. Such changes in the bacterial structure and function were accompanied by disturbances in the composition of the herbaceous plant species layer. These results highlight the role of AM symbiosis in the processes involved in soil bio-functioning and plant coexistence and in afforestation programmes with exotic tree species that target preservation of native plant diversity.     

The impact of elevated carbon dioxide on the phosphorus nutrition of plants: a review

Background Increasing attention is being focused on the influence of rapid increases in atmospheric CO₂ concentration on nutrient cycling in ecosystems. An understanding of how elevated CO₂ affects plant utilization and acquisition of phosphorus (P) will be critical for P management to maintain ecosystem sustainability in P-deficient regions.Scope This review focuses on the impact of elevated CO₂ on plant P demand, utilization in plants and P acquisition from soil. Several knowledge gaps on elevated CO₂-P associations are highlighted.Conclusions Significant increases in P demand by plants are likely to happen under elevated CO₂ due to the stimulation of photosynthesis, and subsequent growth responses. Elevated CO₂ alters P acquisition through changes in root morphology and increases in rooting depth. Moreover, the quantity and composition of root exudates are likely to change under elevated CO₂, due to the changes in carbon fluxes along the glycolytic pathway and the tricarboxylic acid cycle. As a consequence, these root exudates may lead to P mobilization by the chelation of P from sparingly soluble P complexes, by the alteration of the biochemical environment and by changes to microbial activity in the rhizosphere. Future research on chemical, molecular, microbiological and physiological aspects is needed to improve understanding of how elevated CO₂ might affect the use and acquisition of P by plants.     

Glutathione-dependent enzyme activities and concentrations of glutathione,vitamin E and sulfhydryl groups in barbel (Barbus barbus) and its intestinal parasite Pomphorhynchus laevis (Acanthocephala)

Barbel (Barbus barbus) is the final host of the adult worm Pomphorhynchus laevis (Acanthocephala), one of the most abundant and widespread intestinal parasites of European freshwater fish. During the course of the present study, we analyzed the activities of the glutathione-dependent enzymes glutathione peroxidase (GSH-Px), glutathione reductase (GR) and the phase II biotransformation enzyme glutathione-S-transferase (GST) as well as the concentrations of total glutathione (GSH), sulfhydryl (SH) groups and vitamin E (Vit E) in the liver and intestine of B. barbus and in its intestinal parasite P. laevis. The fish were caught from the Danube River (Serbia) in spring and summer. We detected that GSH-Px activity in fish liver was higher in spring. GR activity was significantly higher in spring in all investigated samples, while GST activity was significantly higher in spring in fish liver and in the parasite. At that time, GST activity was ten times higher in the parasite than in fish tissues. The concentration of GSH was increased in barbel liver in spring. In summer, the concentration of SH groups was significantly increased, while the concentration of Vit E was significantly decreased in fish tissues and in the parasite. We performed Canonical Discriminant Analysis, which revealed differentiation among the examined tissues during both seasons based on the all measured antioxidant components. We found that the seasonal patterns of antioxidant defense in the parasite are closely correlated with seasonal variation and physiological change in the host and represent the parasite's adaptation to changes in the host's antioxidant system. The present investigation contributes to general knowledge and provides a basis for future studies of glutathione-dependent enzymes and non-enzymatic low molecular mass antioxidants as potential biomarkers for monitoring the influence of the environment on fishes and their parasites.     

Effects of chemical control agents and microbial biocontrol agents on numbers of non-target microbial soil organisms: a meta-analysis

Our aim was to investigate the non-target effects on soil micro-organisms in agricultural environments caused by chemical control agents (CCAs) and microbial biocontrol agents (mBCAs), including the recovery from these effects. This was a desk study in which quantifiable endpoints, such as numbers of colony forming units (CFU), were derived from a series of studies and the combined data then analysed with a meta-regression analysis. Three analyses of the same dataset were performed. The first analysis, which was performed at the level of the CCAs and mBCAs in general, revealed that the effects of CCAs differed significantly from those of mBCAs. The second analysis, which included the type of non-target group (bacteria, fungi, actinomycetes, and protozoa) as additional input, revealed that mBCAs have greater effects than CCAs on fungi at study initiation, that CCAs had greater effects than mBCAs on bacteria and protozoa and that when effects were measured, recovery occurred within 100 days post-treatment initiation. The final analysis, which included the type of CCA (fungicide, insecticide, herbicide) or mBCA (antagonist) as additional input, revealed that (1) antagonists had a greater effect on fungi than insecticides and fungicides, (2) insecticides and to a lesser extent fungicides had a larger effect on bacteria than fungicides and antagonists, and (3) recovery of the CFU occurred within 100 days for all types of pesticides, mBCAs as well as CCAs, and for all non-target groups. The findings are discussed in view of the regulatory context of admittance of mBCAs to the market.     

The impact of different operating conditions on membrane fouling and EPS production

The main goal of this research was to investigate how different factors influence membrane fouling. The impact of the different concentrations of activated sludge and the amount of extracellular polymer substances (EPS) were monitored. Two pilot plants with submerged membrane modules (hollow fiber and flat sheet) were operated and the raw wastewater was used.Humic substances were identified as the major components of EPS in the activated sludge (more than 34%) in both pilot plants. As the basic constituent in permeate, humic substances were identified as the most dominant components in the effluent (61%) in both pilot plants. Conversely, proteins were mostly analyzed in permeate and supernatant below the detection limit. The total amount of EPS [mg g⁻¹ (VSS)] was similar for concentrations of activated sludge 6, 10 and 14 g L⁻¹. Carbohydrates were identified as the component of EPS which tends most to clog membranes.     

An integrative method for identifying the over-annotated protein-coding genes in microbial genomes

The falsely annotated protein-coding genes have been deemed one of the major causes accounting for the annotating errors in public databases. Although many filtering approaches have been designed for the over-annotated protein-coding genes, some are questionable due to the resultant increase in false negative. Furthermore, there is no webserver or software specifically devised for the problem of over-annotation. In this study, we propose an integrative algorithm for detecting the over-annotated protein-coding genes in microorganisms. Overall, an average accuracy of 99.94% is achieved over 61 microbial genomes. The extremely high accuracy indicates that the presented algorithm is efficient to differentiate the protein-coding genes from the non-coding open reading frames. Abundant analyses show that the predicting results are reliable and the integrative algorithm is robust and convenient. Our analysis also indicates that the over-annotated protein-coding genes can cause the false positive of horizontal gene transfers detection. The webserver of the proposed algorithm can be freely accessible from www.cbi.seu.edu.cn/RPGM.