Mariarita Arenella

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere

We studied the molecular diversity of β-glucosidase-encoding genes, microbial biomass, cellulase, N-acetyl-glucosaminidase, β-glucosidase, and β-galactosidase activities in the rhizosphere and bulk soil of two maize lines differing in nitrogen use efficiency (NUE). The maize lines had significant differences in diversity of β-glucosidase-encoding genes in their rhizosphere, and Actinobacteria and Proteobacteria were the dominating phyla in all samples, but representatives of Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Cyanobacteria were also detected. Among the Proteobacteria, β-glucosidase genes from α-, β-, and γ-Proteobacteria were dominant in the rhizosphere of the high NUE maize line, whereas δ-Proteobacteria β-glucosidase genes were dominant in the rhizosphere of the low NUE maize line. The high NUE maize line also showed higher glucosidase activities in the rhizosphere than the low NUE maize line. We concluded that plants with high NUE select bacterial communities in the rhizosphere differing in the diversity of β-glucosidase-encoding genes which likely result in higher C-hydrolyzing enzyme activities. These effects on the diversity of β-glucosidase-encoding genes may influence the C dynamics in the agro-ecosystems.

Enzyme activity and microbial community structure in the rhizosphere of two maize lines differing in N use efficiency

AimsStudy of the changes in soil microbial biomass, enzyme activity and the microbial community structure in the rhizosphere of two contrasting maize lines differing in the nitrogen use efficiency (NUE).MethodsThe Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soil and solution. We also determined microbial biomass, enzyme activities involved in the C, N, P and S cycles, and the microbial community structure using a phylogenetic group specific PCR-DGGE approach in the rhizosphere and bulk soil of both Lo5 and T250 maize lines.ResultsHigh NUE Lo5 maize induced faster inorganic N depletion in the rhizosphere and larger changes in microbial biomass and enzyme activities than the low NUE T250 maize line. The two maize lines induced differences in the studied microbial groups in the rhizosphere, with the larger modifications induced by the high NUE Lo5 maize line.ConclusionsThe Lo5 maize line with higher NUE induced larger changes in soil chemical properties and in the enzyme activity, soil microbial biomass and community structure than the low NUE T250 maize line, probably due to differences in the root exudates of the two maize lines.

Interactions between proteins and humic substances affect protein identification by mass spectrometry

Soil proteomics is facing problems such as low yields of protein extraction from soil and low protein identification rates as compared to theoretical estimates of soil proteome. This work aimed to evaluate the effect of soil-borne humic substances (HS) on the identification of model proteins with different properties, such as myoglobin (Mb), α-glucosidase (αG), and β-glucosidase (βG), by using electrophoretic and ESI- and MALDI-mass spectrometry (MS) methodologies. Results showed that the contact between proteins and HS did not alter protein electrophoretic mobility but led to protein modifications that affected protein identification by MS. The decrease in protein identification parameters was more evident for Mb than for αG and βG, probably due to its lower molecular weight and less complex molecular structure. Analysis of MS data indicated that hydrophobic interactions could be responsible for the observed effects of contact between proteins and HS.

Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil

We studied the microbial functional diversity, biochemical activity, heavy metals (HM) availability and soil toxicity of Cd, Pb and Zn contaminated soils, kept under grassland or short rotation coppice (SRC) to attenuate the risks associated with HM contamination and restore the soil ecological functions. Soil microbial functional diversity was analyzed by the GeoChip, a functional gene microarray containing probes for genes involved in nutrient cycling, metal resistance and stress response. Soil under SRC showed a higher abundance of microbial genes involved in C, N, P and S cycles and resistance to various HM, higher microbial biomass, respiration and enzyme activity rates, and lower HM availability than the grassland soil. The linkages between functional genes of soil microbial communities and soil chemical properties, HM availability and biochemical activity were also investigated. Soil toxicity and N, P and Pb availability were important factors in shaping the microbial functional diversity, as determined by CCA. We concluded that in HM contaminated soils the microbial functional diversity was positively influenced by SRC management through the reduction of HM availability and soil toxicity increase of nutrient cycling. The presented results can be important in predicting the long term environmental sustainability of plant-based soil remediation.

Nitrate induction and physiological responses of two maize lines differing in nitrogen use efficiency: effects on N availability, microbial diversity and enzyme activity in the rhizosphere

AimThe rate of nitrate (NO3−) uptake and changes in rhizosphere properties were studied growing seedlings of two maize inbred lines differing in nitrogen use efficiency (NUE) in rhizoboxes.ResultsChanges in NO3− uptake rates occurred in response to anion addition (induction) in seedlings grown both in hydroponic culture and in soil in rhizoboxes. The characterization of root exudate composition showed a line-specific metabolite profile, which was also affected by NO3− availability. The induction affected respiration, nitrification, ammonification and enzyme activities of the rhizosphere. Furthermore, the composition of rhizosphere bacterial communities of the two maize lines differed suggesting the selective capacity of plants.ConclusionsOverall, results showed a strong and fast modification of rhizospheric soil properties in response to physiological changes in plants caused by fluctuating NO3− availability.

Contact with soil-borne humic substances interfere with the prion identification by mass spectrometry

We studied the effects of humic substances (HS) extracted from soil on the identification of the recombinant ovine prion protein (RecPrP) by denaturing (sodium dodecyl sulfate polyacrylamide gel electrophoresis [SDS-PAGE]) and native PAGE (N-PAGE), and mass spectrometry (MS), at various HS to RecPrP contact ratios. The results showed that the contact with HS did not alter RecPrP electrophoretic mobility but affected protein identification by MS. Contact between RecPrP and HS resulted in a lower coverage percentage of specific RecPrP domains that led to a prion misidentification, more evident after N-PAGE than SDS-PAGE. The analysis of the nonidentified protein domains suggests that lower quality of RecPrP identification could be due to hydrophobic interactions between the prion protein and HS, but the mechanism by which HS hamper the correct identification of RecPrP remains to be established. Our results may have implications in the prion environmental risk assessment.