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Crop decline is a progressive soil health reduction commonly associated to the specialized cultivations. As a series of biotic factors are involved in this phenomenon, it can be controlled with essentially agronomic methods, the impact of winter cover crops on early growth at subsequent vegetable crops was investigated in a two-year field study. Barley and hairy vetch were incorporated into the soil following two mechanical terminations of cover crops (green manure and green mulching). Immediately after, tomato and zucchini seedlings were transplanted and grown for 28 days. The above-ground biomass of the vegetables was taken as indicator of crop response to pre-plant treatments, whilst root colonizing fungi and rhizosphere bacteria were the two analyzed soil microbial components. Root-colonizing fungi were evaluated using culture-based methods, bacteria were analyzed by amplification of rhizosphere soil DNA with 16S rDNA, then processed with PCR-DGGE. Tomato and zucchini growth response after vetch was always significantly higher than after barley regardless of mechanical termination. Rhizosphere bacterial communities differed significantly between cover crops and this differences was maintained also in the subsequent vegetable crops. Root-colonizing fungi differed between barley and vetch, although they shared most species (70%) such as Pythium spp., binucleate Rhizoctonia AG-A and several Fusarium spp. The latter three fungal groups were also found most abundant in tomato and zucchini roots. Pathogenicity test showed that tomato was more susceptible than zucchini to Pythium , Rhizoctonia solani , Fusarium oxysporum and Fusarium spp. and that their relationship with vegetable plants varied from pathogenic to neutral, up to mutualistic in the case of Rhizoctonia AG-A. These findings indicate difficulty to identify specific biotic agents responsible of crop decline. Tomato and zucchini showed an undoubted growth improvement after legume; however, a certain specificity of Cylindrocarpon -like fungi and Phoma spp. to hairy vetch suggests that, when exploiting benefit of this cover crop for mitigating yield decline of vegetable crops, legume should alternate cereal and other botanically distant genera in rotation. [ABSTRACT FROM AUTHOR]

The soils impacted by sea animal excreta are important sources of nutrients in Antarctic terrestrial ecosystems, and soil microorganisms are the principal drivers of carbon and nitrogen cycling. However, microbial diversity and enzyme activities in these soils have still received little attention. In this paper, we investigated the distribution characteristics of bacterial community in four penguin and seal colony soil profiles collected in East Antarctica, using 16S rDNA-DGGE and real-time quantitative PCR. Soil microbial biomass carbon (C), soil respiration (SR), and enzyme activities involved in carbon, nitrogen, and phosphorus metabolisms were also measured. Overall soil C, SR, enzyme activities, and bacterial abundance decreased with depth. The bacterial abundance had a significant correlation with soil organic carbon and total nitrogen and highly corresponded to the relative content of penguin guano or seal excreta in these soil profiles. The 16S rDNA-DGGE revealed the complicated bacterial community structure in penguin and seal colony soils, and the band richness and dominant bands decreased with soil depth. Cluster analysis of DGGE profiles indicated that bacterial community in those soil profiles were divided into four main categories with the bacterial genetic similarity of 22 %, and the majority of the sequenced bands were Proteobacteria ( α, β, γ), Actinobacteria, Bacteroidetes, Deinococcus- Thermus, Chloroflexi, and Firmicutes. Our results indicated that the deposition of penguin guano or seal excreta, which caused the variability in soil soil organic carbon, total nitrogen, pH, and soil moisture, might have an important effect on the vertical distribution pattern of bacterial abundance and diversity in Antarctic soil profiles. [ABSTRACT FROM AUTHOR]

This study aimed to identify bacterial community structures in the Vaal River using PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) and high-throughput sequencing. The impact of physico-chemical characteristics on bacterial structures was investigated through multivariate analysis. Samples were collected from 4 sampling stations along the Upper Vaal River during winter (June 2009) and summer (December 2010). Physico-chemical analysis was conducted on-site. Additional physico-chemical data were obtained from statutory bodies. DNA was directly isolated from water samples and PCR amplified using universal bacterial primer pairs. PCR products were subjected to DGGE fingerprinting and high-throughput sequencing, followed by Shannon-Weaver diversity calculations, cluster analysis and multivariate analysis. Physico-chemical parameters did not exceed the prescribed South African water quality standards for domestic use, aquatic ecosystems, livestock watering and irrigation. DGGE banding patterns revealed similar bacterial community structures for 3 of the 4 sampling stations. PCA and RDA indicated that pH, water temperature and inorganic nutrient concentrations could be used to explain changes in bacterial community structures. High-throughput sequencing data showed that bacterial assemblages were dominated by common freshwater groups: Cyanobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Other freshwater phyla such as Deltaproteobacteria, Epsilonbacteria, Acidobacteria, Verrucomicrobia, Firmicutes, Fusobacteria, Flavobacteria and Fibrobacteres were found in low proportions. This study provides an overview of the dominant bacterial groups in the Upper Vaal River and the impact of environmental changes on bacterial diversity. [ABSTRACT FROM AUTHOR]

Abstract: An effective method for grouping acetic acid bacteria (AAB) genera was defined and evaluated as a tool for preliminary screening of the major AAB species involved in vinegar production. Acetobacter, Gluconobacter, Gluconacetobacter, Asaia, Neoasaia, Saccharibacter, Frateuria and Kozakia AAB strains were screened on the basis of the 16S rDNA sequences using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique. The DGGE profile of all the strains tested, consisted of one single band of approximately 330 bp for each strain and allowed their clustering. The results obtained clearly reflected in silico phylogenetic analysis of the AAB species used in this study, in fact, the species with a higher 16S rDNA sequence homology showed a similar electrophoretic profile. In particular almost all the species belonging to the genus Gluconacetobacter showed a DGGE pattern nearly identical and well distinct from all the other AAB genera. Furthermore by PCR-DGGE it was possible to clearly group the species more frequently recovered from vinegar fermentation which are mainly distributed in the genera Acetobacter, Gluconobacter and Gluconacetobacter. [Copyright &y& Elsevier]

Understanding the microbial processes affecting the mobility of Au is important in the development of biogeochemical models describing the formation of secondary anomalies and Au grains in soils and deeper regolith materials. This study characterizes bacterial activity in auriferous soils that is linked to the microbially mediated solubilization of Au, as a result of production and consumption of free amino acids, which can form stable complexes with Au. Through the application of 16S rDNA fingerprinting and community level physiological profiling (CLPP), concurrently with Au mobility data, microcosm experiments have demonstrated the role that mobile Au plays in determining the structure and function of bacterial communities in auriferous soils. The bacterial community of auriferous soils displayed genetic differences compared to non-auriferous (background) soils associated with the appearance of Methylocella sp., Arthrobacter sp. and Bacillus sp., as well as functional differences in the utilization of D-Cellobiose, L-Serine, L-Phenylalanine, L-Arginine and N-Acetyl-D-Glucosamine. These results suggest that soil bacterial communities are linked to biogeochemical Au cycling, and that microbial fingerprinting analyses may be used as a screening tool in Au exploration to differentiate auriferous from background terrains. [ABSTRACT FROM AUTHOR]