Data for: Microbial responses to selected pharmaceuticals in agricultural soils: Microcosm study on the roles of soil, treatment and time

This dataset evaluates microbial responses to pharmaceuticals in agricultural soils which may improve essentially our understanding of micropollutants fate and their potential implications to the environmental and human health. In this study, we focused on immediate (1 d), short- (13 d) and long-term effects (61 d) of pharmaceuticals amendment on microbial changes in seven soils differing in physical chemical properties. The data include dictionaries of used soils, treatments, parent compounds and their metabolites, and measured fatty acids. Degradation of the individual pharmaceuticals as well as their mixture are shown in folder "analytics", and raw observation data for basal respiration and phospholipid fatty acids are given in respiration.csv and PLFA.csv. The code to run these data will be publicly open on GitHub upon publishing the scientific article of the same name.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Mapping spatial patterns of denitrifiers for bridging community ecology and microbial processes along environmental gradients

Affiche, résuméWhile there is ample evidence that microbial processes can exhibit large variations at a field scale, very little is known about the spatial distribution of the communities mediating these processes. The objective of this study was to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We used geostatistical modeling to map the distribution of size and activity of the denitrifier community in the pasture. Size of the denitrifier community was estimated by PCR quantification of the denitrification gene copy numbers while its activity was estimated by measuring potential denitrification activity and potential N2O emissions. We found non-random distribution patterns of the size and of the activity of the denitrifier community were observed with a field-scale spatial dependence. The soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N2O production but not on the size of the denitrifier community. The relative abundance of bacteria possessing the nosZ gene encoding the N2O reductase within the total bacterial community was a strong predictor of the N2O/N2 ratio. Overall, our results indicated that patterns of distribution of denitrifiers can be modelled at the field scale. Characterization of such pattern at a field-scale constitutes the first step in modelling distribution of functional bacterial communities at a scale compatible with land management strategies. The abundance of most denitrification genes was not correlated with potential denitrification activity or potential N2O production. However, the relative abundance of bacteria possessing the nosZ gene in the total bacterial community was a strong predictor of the N2O/(N2+N2O) ratio, providing evidence for a relationship between ecosystem processes and bacterial community composition

Survival of genetically marked Escherichia coli O157:H7 in soil as affected by soil microbial community shifts

A loamy sand soil sampled from a species- rich permanent grassland at a long- term experimental site ( Wildekamp, Bennekom, The Netherlands) was used to construct soil microcosms in which the microbial community compositions had been modified by fumigation at different intensities ( depths). As expected, increasing depth of fumigation was shown to result in progressively increasing effects on the microbiological soil parameters, as determined by cultivation- based as well as cultivation- independent ( PCR- DGGE, PLFA) methods. Both at 7 and at 60 days after fumigation, shifts in the bacterial, fungal and protozoan communities were noted, indicating that altered community compositions had emerged following a transition phase. At the level of bacteria culturable on plates, an increase of the prevalence of bacterial r- strategists was noted at 7 days followed by a decline at 60 days, which also hinted at the effectiveness of the fumigation treatments. The survival of a non- toxigenic Escherichia coli O157: H7 derivative, strain T, was then assessed over 60 days in these microcosms, using detection via colony forming units counts as well as via PCR- DGGE. Both data sets were consistent with each other. Thus, a clear effect of fumigation depth on the survival of the invading strain T was noted, as a progressive increase of depth coincided with a progressively enhanced inoculant survival rate. As fumigation depth was presumably inversely related to community complexity, this was consistent with the hypothesis that soil systems with reduced biological complexity offer enhanced opportunities for invading microbial species to establish and persist. The significance of this finding is discussed in the light of the ongoing discussion about the complexity - invasiveness relationship within microbial communities, in particular regarding the opportunities of pathogens to persist

Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils

Background and aims: Livestock grazing is a widely practiced land-use regime that can impose lingering effects on global biogeochemical cycles. However, elucidating the mechanisms of related eco-processes, which are largely mediated by the microbial community, remains challenging. Methods: Here, we collected soil samples from two Tibetan grassland sites subjected to grazing in winter followed by a 3-month recovery. We then evaluated functional potentials of microbial communities via a metagenomic tool known as GeoChip 4.0. Results: Significant alterations were detected in post-grazing grassland soils, and further analysis showed that plant diversity was the best indicator of alterations in functional potentials. Relative abundances of labile C degradation genes decreased at the 3400-m site, but those of recalcitrant C degradation genes increased, which could be explained by the higher soil recalcitrant C input owing to their being substantially more forbs species at this site. Nitrification genes decreased at both sites, probably owing to increased soil moisture conducive to oxygen-limiting conditions. Relative abundance of denitrification genes increased at the 3200-m site, concomitant with increased N2O emissions. Conclusions: These results demonstrated that functional gene compositions of the microbial community were altered in post-grazing grassland soils, and linked to soil biogeochemical processes