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Byline: Susanne Klammer (Institute of Microbiology, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria); Brigitte Knapp (Institute of Microbiology, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria); Heribert Insam (Institute [...]

Ethidium monoazide and propidium monoazide were used to develop a new DNA extraction technique to discriminate between alive and dead bacterial cells. The method could be used to study anaerobic fermentor sludge and compare the results to a conventional microbiological approach.

Carbon ( C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and diversity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by 13 C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal ( AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing ( RNA- SIP), in combination with real-time PCR and PCR- DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the 13 C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes. [ABSTRACT FROM AUTHOR]

During composting, the degradation of organic waste is accompanied and driven by a succession of microbial populations exhibiting a broad range of functional capabilities. Detailed inventories of the microbial communities in mature compost, however, are not available. Mature composts, originating from biowaste as well as sewage sludge and anaerobic sludge, were studied by denaturing gradient gel electrophoresis-fingerprints after polymerase chain reaction (PCR) amplification of the 16S rRNA genes using three different universal primer pairs, as well as by differential scanning calorimetry and thermogravimetry. The composts of different origin had different bacterial communities. The influence of different 16S rDNA primer sets on the same batches of compost DNA was evaluated. The clearest separation of different compost types was obtained by using the PCR primer pair 338f + 518r which is suggested for future applications. Communities from the different biowaste compost samples clustered together and could be separated from sewage sludge communities indicating the establishment of different microbial consortia. A similar differentiation of composts was found with the thermogavimetric analyses. It may thus be concluded that the resulting humus quality is closely linked to the microbial communities involved. [ABSTRACT FROM AUTHOR]

Background, Aims, and Scope. The genetic structure and the functionality of soil microbes are both important when studying the role of soil in the C cycle in elevated CO2 scenarios. The aim of this work was to investigate the genetic composition of the fungal community by means of PCR-DGGE and the functional diversity of soil micro-organisms in general with MicroResp-based community level physiological profiling (CLPP) in a poplar plantation (POPFACE) grown under elevated [CO2] with and without nitrogen fertilization. Materials and Methods. The POPFACE experimental plantation and FACE facility are located in central Italy, Tuscania (VT). Clones of Populus alba, Populus nigra and Populus x euramericana were grown, from 1999 to 2004, in six 314 m² plots treated either with atmospheric (control) or enriched (550 μmol mol-1) CO2 with FACE (Free Air CO2 Enrichment) technology in each growing season. Each plot is divided into six triangular sectors, with two sectors per poplar genotype: three species x two nitrogen levels. After removal of the litter layer one soil core per genotype (10 cm wide, 20 cm depth) was taken inside each of the three sectors in each plot, for a total of 36 soil cores (3 replicates x 2 [CO2] x 2 fertilization x 3 species) in October 2004 and in July 2005. DNA was extracted with a bead beating procedure. 18S rDNA gene fragments were amplified with PCR using fungal primers (FR1 GC and FF390). Analysis of CLPP was performed using the MicroResp method. Carbon substrates were selected depending on their ecological relevance to soil and their solubility in water. In particular rhizospheric C sources (carboxylic acids and carbohydrates) were chosen considering the importance of root inputs for microbial metabolism. Results. The fertilization treatment differentiated the fungal community composition regardless of elevated [CO2] or the poplar species; moreover the number of fungal species was lower in fertilized soil. The effect of elevated [CO2] on the fungal community composition was evident only as interaction with the fertilization treatment as, in N-sufficient soils, the elevated [CO2] selected a different microbial community. For CLPP, the different poplar species were the main factors of variation. The FACE treatment, on average, resulted in lower C utilization rates in un-fertilized soils and higher in fertilized soils. Discussion. Fungal biomass and fungal composition depend on different factors: from previous studies we know that the greater quantity and the higher C/N ratio of organic inputs under elevated [CO2] influenced positively the fungal biomass both in fertilized and in un-fertilized soil, whereas nitrogen availability resulted to be the main determinant of fungal community composition in this work, Whole active microbial community was directly influenced by the soil nutrient availability and the poplar species. Under elevated CO2 the competition for N with plants strongly affected the microbial communities, which were not able to benefit from added rhizospheric substrates, Under N-sufficient conditions, the increase of microbial activity due to [CO2] enrichment was related to a more active microbial community, favoured by the current availability of C and N. Conclusions. Different factors influenced the microbial community at different levels: poplar species and root exudates affected the functional properties of the microbial community, while the fungal specific composition (as seen with DGGE) remained unaffected. On the other hand, factors such as N and C availability had a strong impact on the community functionality and composition.… [ABSTRACT FROM AUTHOR]

Abstract: Composts are increasingly used as environmentally safe biofertilizers in sustainable agriculture all over the world. Although it is well known that composts may contribute to soil vitality and sustainability, and in the enhancement of various soil microbiological processes, little is known about their direct or indirect effects on a microbial-community or population level. Ammonia oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and plays an important role in the global nitrogen cycle. Here, we studied the diversity and community composition of ammonia oxidizers in a long-term crop rotation field experiment (>10 years) where four major types of compost (from organic waste, cattle manure, green waste and sewage sludge) had been applied annually. The methods used ranged from PCR-DGGE (denaturing gradient gel electrophoresis) and cloning of 16S rDNA fragments to quantitative real-time PCR. Cluster analysis of DGGE profiles differentiated between the microbial communities of composts, compost-treated soils and mineral-fertilized soils. The community composition of the composts was not reflected in the community composition of the compost-treated soils. Sequencing of screened clones revealed a characteristic AOB community structure for the representative soil sample and the four composts. All AOB-like sequences grouped within the Nitrosospira cluster 3 and 4 and within the Nitrosomonas cluster 6 and 7. The average AOB abundance in compost-treated soils was two times higher than in mineral-fertilized soils (4.3×107 and 1.9×107, respectively). Our data suggest that composts do not leave direct microbial imprints in soils after long-term amendment, but an indirect effect on the AOB community was evident. [Copyright &y& Elsevier]

Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and diversity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by (13) C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the (13) C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes., (© 2012 Blackwell Publishing Ltd.)