Treated agro-industrial wastewater irrigation of tomato crop: Effects on qualitative/quantitative characteristics of production and microbiological properties of the soil

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Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard

<p>Abstract</p> <p>Background</p> <p>Polar bears (<it>Ursus maritimus</it>) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81°N, 10-33°E). In addition the level of <it>bla</it>_TEMalleles, encoding ampicillin resistance (amp^r) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006.</p> <p>Results</p> <p>A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum <it>Firmicutes</it>, with 160 sequences identified as <it>Clostridiales </it>and one sequence identified as unclassified <it>Firmicutes</it>. The majority of the sequences (70%) were affiliated with the genus <it>Clostridium</it>. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 × 10⁴to 1.6 × 10⁶colony forming units (cfu)/ml for the rectum swabs and 4.0 × 10³to 1.0 × 10⁵cfu/g for the faeces samples. The proportion of amp^rbacteria ranged from 0% to 44%. All of 144 randomly selected amp^risolates tested positive for enzymatic β-lactamase activity. Three % of the amp^risolates from the rectal samples yielded positive results when screened for the presence of <it>bla</it>_TEMgenes by PCR. <it>Bla</it>_TEMalleles were also detected by PCR in two out of three total faecal DNA samples from polar bears.</p> <p>Conclusion</p> <p>The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to <it>Firmicutes</it>. Furthermore, only low levels of <it>bla</it>_TEMalleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.</p

Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography

<p>Abstract</p> <p>Background</p> <p>BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (<it>Bacillus cereus</it>; <it>Escherichia coli</it>; isolates of the family <it>Geodermatophilaceae</it>). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of <it>Modestobacter multiseptatus </it>isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of <it>Streptococcus thermophilus </it>isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia.</p> <p>Results</p> <p>Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (<it>p </it>< 0.004 and <it>p </it>< 0.00003) and in capillary electrophoresis (compared only with HEX, <it>p </it>< 2 × 10^-7). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped <it>M. multiseptatus </it>strains according to the microsite of isolation and <it>S. thermophilus </it>strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used.</p> <p>Conclusion</p> <p>F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.</p

Sustainable Water Management and Wetland Restoration Strategies in Northern China

This book depicts the results of a research project in northern China, where an international and interdisciplinary team of researchers from Italy, Germany and China has applied a broad range of methodology in order to answer basic and applied research questions and derive comprehensive recommendations for sustainable water management and wetland restoration. The project primarily focused on ecosystem services, e.g. the purification of water and biomass production. In particular, the ecosystem function and use of reed (Phragmites australis) and the perception as well as the value of water as a resource for Central Asia's multicultural societies was analysed

Sustainable Water Management and Wetland Restoration Strategies in Northern China

This book depicts the results of a research project in northern China, where an international and interdisciplinary team of researchers from Italy, Germany and China has applied a broad range of methodology in order to answer basic and applied research questions and derive comprehensive recommendations for sustainable water management and wetland restoration. The project primarily focused on ecosystem services, e.g. the purification of water and biomass production. In particular, the ecosystem function and use of reed (Phragmites australis) and the perception as well as the value of water as a resource for Central Asia's multicultural societies was analysed

Temporal shifts in endophyte bacterial community composition of sessile oak (Quercus petraea) are linked to foliar nitrogen, stomatal length, and herbivory

We studied the relationship between plant functional foliar traits and the endophytic bacterial communities associated in trees, taking the example of sessile oak (Quercus petraea (Matt.) Liebl). Forty-five samples with replicates of eight leaves per sample were collected in spring, summer and autumn. Bacterial community diversity was analyzed via Automated Ribosomal Intergenic Spacer Analysis (ARISA). The leaf traits specific leaf area, level of herbivory, stomatal number, stomatal length, carbon and nitrogen concentration were measured for the leaves of each sample. For statistical analysis, linear mixed effect models, the Canonical Correlation Analysis (CCA) and Non-Parametric Multivariate Analysis of Variance (NPMANOVA) were applied. Herbivory, nitrogen and carbon concentration were significantly different in autumn compared to spring and summer (p value < 0.05), while stomatal length was differentiated between spring and the other two seasons (p value < 0.01). The seasonal differentiation of the bacterial community structure was explained by the first and second axes (29.7% and 25.3%, respectively) in the CCA. The bacterial community structure significantly correlated with herbivory, nitrogen concentration and stomatal length. We conclude that herbivory, nitrogen content, and size of stomatal aperture at the leaf level are important for endophyte colonization in oaks growth in alpine forest environments

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment.

Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition

Environmental micro-niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield

The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m2 area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co-occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high-throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche-specific role of the micro-environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico-chemical and micro-climatic variations at the site-spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis

Biodiversity of prokaryotic communities in sediments of different sub-basins of the Venice lagoon

Microbial community structure and diversity in the wide and shallow Venice lagoon were assessed, before the construction of mobile dams, in nine stations representative of different four sub-basins previously selected on the basis of international guidelines for sediment quality. The sediments were mostly anoxic and colonised by microbial communities whose species richness was quantitatively correlated to total elemental sulphur and acid volatile sulphide. Automated Ribosomal Intergenic Spacer Analysis clustered the stations in three groups. One station for each group has been hence analysed in detail for bacterial and archaeal diversity by the screening of 16S rRNA gene clone libraries. The dominance of Gammaproteobacteria clones (84% with a high proportion of Vibrionaceae, indicator of urban pollution) determined a significant divergence of the station adjacent to industrial and metropolitan areas. Bacteroidetes were widespread especially where prairies of aquatic plants are located. The other two analysed stations were dominated by bacterial taxa implicated in the sulphur cycle: the anoxygenic photosynthetic Chromatiales, sulphate and sulphur reducing Desulfobacterales and Desulfuromonadales, and members of the Alpha- and Epsilonproteobacteria