Brigitte A. Knapp

Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics

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.

Bacterial community patterns and thermal analyses of composts of various origins.

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.

Recycling of Biomass Ashes: Current Technologies and Future Research Needs

Biomass ash is a final by-product from biomass incineration and is being produced in increasing amounts. Ash contains a variety of macronutrients and micronutrients and thus requires an appropriate recycling strategy. This chapter addresses various recycling strategies and technologies, with a particular focus on a smart combination of wastes from different sources for optimising recycling efficiency.

Recycling of Biomass Ashes

The feasibility of using woody biomass fly ash (WBFA) as a mineral admixture in cement-based materials was investigated. This fly ash was characterized for chemical composition and used to prepare a cement blend with 70 wt% Portland cement and 30 wt% WBFA. Cubic specimens were cast from a blended cement paste (water-to-binder ratio 0.50) and, after 28 days of curing at 20 C and 100% relative humidity, these specimens were tested for heavy metal leachability through the use of a sequential leaching protocol, at a constant pH of leachant (deionized water; pH 6.0). It was found that, except for the chloride content, the WBFA is able to meet the European chemical requirements established for reuse of coal fly ash in cement-based materials. Although the WBFA is characterized by a significant content of heavy metals of particular environmental concern (Cd, Cr, Cu, Ni, Pb, Zn), the results of the monolith leaching test have shown a good immobilization capacity of such metals by the cementitious matrix and, consequently, a good environmental quality of the blended cement investigated.

Application of denaturing gradient gel electrophoresis for analysing the gut microflora of Lumbricus rubellus Hoffmeister under different feeding conditions

The earthworm, Lumbricus rubellus, plays an essential role in soil ecosystems as it affects organic matter decomposition and nutrient cycling. By ingesting a mixture of organic and mineral material, a variety of bacteria and fungi are carried to the intestinal tract of the earthworm. To get a better understanding of the interactions between L. rubellus and the microorganisms ingested, this study tried to reveal if the diet affects the composition of the gut microflora of L. rubellus or if its intestinal tract hosts an indigenous, species-specific microbiota. A feeding experiment with L. rubellus was set up; individuals were collected in the field, transferred to a climate chamber and fed with food sources of different quality (dwarf shrub litter, grass litter or horse dung) for six weeks. DNA was extracted from the guts of the earthworms, as well as from the food sources and the surrounding soil, and further analysed by a molecular fingerprinting method, PCR-DGGE (Polymerase Chain Reaction -- Denaturing Gradient Gel Electrophoresis). We were able to demonstrate that the gut microbiota was strongly influenced by the food source ingested and was considerably different to that of the surrounding soil. Sequencing of dominant bands of the bacterial DGGE fingerprints revealed a strong occurrence of y-Proteobacteria in all gut samples, independent of the food source. A specific microflora in the intestinal tract of L. rubellus, robust against diet changes, could not be found.

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year.

Substrate-induced volatile organic compound emissions from compost-amended soils

The agronomic effects of composts, mineral fertiliser and combinations thereof on chemical, biological and physiological soil properties have been studied in an 18-year field experiment. The present study aimed at tracing treatment effects by evaluating the volatile organic compound (VOC) emission of the differently treated soils: non-amended control, nitrogen fertilisation and composts (produced from organic waste and sewage sludge, respectively) in combination with nitrogen fertiliser. Microbial community structure was determined by denaturing gradient gel electrophoresis (DGGE). Aerobic and anaerobic soil VOC emission was determined after glucose amendment using proton transfer reaction–mass spectrometry (PTR-MS). After inducing VOC production by substrate (glucose) addition and at the same time reducing oxygen availability to impair degradation of the produced VOCs, we were able to differentiate among the treatments. Organic waste compost did not alter the VOC emissions compared to the untreated control, whilst sewage sludge composts and mineral fertilisation showed distinct effects. This differentiation was supported by DGGE analysis of fungal 18S rDNA fragments and confirms earlier findings on bacterial communities. Three major conclusions can be drawn: (1) VOC patterns are able to discriminate among soil treatments. (2) Sewage sludge compost and mineral fertilisation have not only the strongest impact on microbial community composition but also on VOC emission patterns, but specific tracer VOCs could not be identified. (3) Future efforts should aim at a PTR-MS-linked identification of the detected masses.

Bacterial community composition of the gut microbiota of Cylindroiulus fulviceps (diplopoda) as revealed by molecular fingerprinting and cloning

Bacterial clone libraries of the gut microbiota of nurtured and starved Cylindroiulus fulviceps specimens displayed the predominance of the phyla Bacteroidetes (55 and 37 %, respectively) and Proteobacteria (40 and 35 %, respectively) and a high similarity to bacteria previously detected in the intestinal tract of termites and beetles, which are known to harbor symbiotic bacteria essential for digestive activity. Bacterial isolates were dominated by Proteobacteria (74 %), followed by members of the phyla Actinobacteria, Firmicutes and Bacteroidetes. PCR-DGGE fingerprints of the gut samples showed that intestinal bacteria were affected by starvation, although the change was not significant.

Do Composts Affect the Soil Microbial Community

Compost amendments have been shown to provide manifold benefits, as long as compost of good quality is used and care is taken not to accumulate heavy metals or organic pollutants as a consequence of repeated applications. Among the advantages of compost as soil amendment is its potential to maintain soil organic matter, foster nutrient availability, suppress plant diseases and increase soil microbial abundance and activity, thus enhancing soil quality and fertility. However, only little is known about how compost amendments act as microbial inoculum to the soil and if the compost-borne microflora leaves a long-term imprint on soil microbial communities. In this chapter, it will be analysed if and to what extent soil microbial biomass, activity and community structure are affected by compost amendments. A long-term field study, in which four different composts have been applied annually since 1991, will be presented in detail.

Palatability of selected alpine plant litters for the decomposer Lumbricus rubellus (Lumbricidae).

On alpine pastureland the decline in large-bodied earthworm numbers and biomass after abandonment of management might be the result of a shift from highly palatable grass litter to poorly digestible leaf litter of dwarf shrubs. To test this hypothesis, we analysed nitrogen, phosphorous and total phenolic contents of fresh and aged litter of eight commonly occuring alpine plant species and compared consumption rates of these food sources in a controlled feeding experiment with Lumbricus rubellus (Lumbricidae). Furthermore, we analysed the microbial community structure of aged litter materials to check for a relationship between the microbial characteristics of the different plant litter types and the food choice of earthworms. Plant litters differed significantly in their chemical composition, earthworms, however, showed no preference for any litter species, but generally rejected fresh litter material. Microbial community structures of the litter types were significantly different, but we could find no evidence for selective feeding of L. rubellus. We conclude that L. rubellus is a widespread, adaptable ubiquist, which is able to feed on a variety of food sources differing in quality and palatability, as long as they have been exposed to wheathering.