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- Comparative study of the microbial diversity of bulk paddy soil of two rice fields subjected to organic and conventional farmingPublication . Lopes, Ana R.; Faria, Cátia; Prieto-Fernández, Ángeles; Trasar-Cepeda, Carmen; Manaia, Célia M.; Nunes, Olga C.Two adjacent paddies of an experimental rice field, subjected to organic and conventional farming, were characterized aiming the comparative assessment of microbiological variations occurring in the bulk paddy soil over the rice cycle. This study comprehended the simultaneous characterization of general physicochemical soil properties [total carbon and nitrogen, pH (H2O and KCl), C:N ratio and water content], biochemical properties [enzymatic activities and Community Level Physiological Profiles (CLPP)], the estimation of cultivable organisms (enumeration of fast growing heterotrophic bacteria, actinomycetes and fungi) and the assessment of bacterial diversity using a culture-independent method (PCR-DGGE fingerprinting). The linkage of the parameters measured was analysed by canonical correspondence analysis (CCA). CCA ordination plots of the CLPP showed a similar pattern of microbial functional activity in both agronomic management systems, except in June. Enzymatic activity, water content and fungi counts were the main factors affecting the observed CLPP time variation. Such a variation was not expressed by the Shannon and evenness indices, which did not evidence significant differences in the bacterial and functional diversity between or within farming type over the analysed period. The cluster and CCA analyses of the DGGE profiles allowed the distinction of the bacterial communities of both paddies, with temporal variations being observed in the organically managed field but not in the conventional paddy. Enzymatic activity, pH and molinate content were the factors which most contributed to the observed variations. Altogether these results underline the functional redundancy of the rice paddy soil and evidence the temporal variations on the metabolic activity of soil, irrespective of farming type.
- Rhizobacterial communities associated with the flora of three serpentine outcrops of the Iberian PeninsulaPublication . Álvarez-López, Vanessa; Prieto-Fernández, Ángeles; Becerra-Castro, Cristina; Monterroso, Carmela; Kidd, Petra S.Aim Plant -associated bacteria can improve phytoextraction by increasing plant growth and/or metal uptake. This study aimed to characterise the culturable rhizobacterial community associated with two Nihyperaccumulators and to obtain a collection of isolates for application in Ni phytomining. Methods Non-vegetated and rhizosphere soil samples were collected from the Ni-hyperaccumulator Alyssum serpyllifolium ssp. lusitanicum (three populations) and Alyssum serpyllifolium ssp. malacitanum (one population), as well as from non-hyperaccumulating plants (Dactylis glomerata, Santolina semidentata and Alyssum serpyllifolium ssp. serpyllifolium). Rhizobacteria were isolated and characterised genotypically (BOX-PCR, 16S rDNA sequencing) and phenotypically (Ni tolerance, plant growth promoting (PGP) traits, biosurfactant production). Results Hyperaccumulating Alyssum subspecies hosted higher densities of bacteria compared to either nonhyperaccumulators or non-vegetated soil. In some cases hyperaccumulators showed selective enrichment of Nitolerant bacteria. Most bacterial strains belonged to the Actinobacteria phylum and presented Ni resistance. Phosphorus-solubilisers were mostly associated with the hyperaccumulators, siderophore-producers with D. glomerata, and IAA-producers with both these species. Conclusion Taxonomic diversity and phenotypic characteristics were soil-, plant species- and plant population- specific. Moreover, differences were observed between the two Ni-hyperaccumulating subspecies and amongst plant populations. Several strains presented PGP characteristics which could be useful when selecting microorganisms for bioaugmentation trials.
- Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation systemPublication . Lopes, Ana R.; Bello, Diana; Prieto-Fernández, Ángeles; Trasar-Cepeda, Carmen; Manaia, Célia M.; Nunes, Olga C.The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N-2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.