Bedeutung von Struktur und Funktion mikrobieller Gemeinschaften für den Kohlenstoffumsatz im landwirtschaftlich genutzten Boden : Modelluntersuchungen in prozessorientierten Mikrokosmen

The microbial communities in the soil are responsible for material cycling and thus also for maintaining the fertility of agricultural soils. In order to assess the influence of anthropogenic activity, e .g. from the application of pesticides, an the soil, its microflora and the associated material cycles, detailed knowledge is required an the structure and function of microbial communities in soils. In the present study, the microorganisms involved in the conversion of crop residues were investigated in process-oriented microcosms, amongst other procedures, by means of the denaturing gradient gel electrophoresis (DGGE) of the amplified 16S rDNA sections. The humic acids synthesized in the microcosms served as indicators of the quality of the humification process and were analysed by 13C-NMR spectroscopy and gel permeation chromatography (GPC)

Further Development and Applications of GeoChip 3.0 for Microbial Community Analysis

Microarrays constructed with the genes encoding key enzymes involved in various biological and geochemical processes are referred to as functional gene arrays (FGAs), or GeoChip. On the basis of GeoChip 2.0 (He et al., 2007), which contains 24,243 oligonucleotide (50mer) probes and covers >10,000 gene sequences in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, a new generation of GeoChip (GeoChip 3.0) has been developed. GeoChip 3.0 has several new features compared to GeoChip 2.0. First, GeoChip 3.0 cover about 47,000 gene sequences for 292 gene families, and such a coverage allows us to obtain more information about microbial communities and analyze more diverse environmental samples. Second, the homology of automatically retrieved sequences by key words is verified by HUMMER using seed sequences so that any potential unrelated sequences are removed. Third, GeoChip 3.0 includes phylogenic markers, such as gyrB. Fourth, a software package (including databases) has been developed for sequence retrieval, probe and array design, probe verification, array construction, array data analysis, information storage, and automatic update, which greatly facilitate the management of such a complicated array, especially for future update. Fifth, universal standards have been implemented in GeoChip 3.0 so that data normalization and comparison of different samples can be conducted. Finally, genomic standards are also used to quantitatively analyze gene abundance. GeoChip was used to analyze effects of elevated CO2 on belowground microbial communities at BioCON. The results demonstrated that GeoChip 3.0 could provide more capability for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is also particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions

GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

Microarray-based genomic technology has been widely used for microbial community analysis, and it is expected that microarray-based genomic technologies will revolutionize the analysis of microbial community structure, function and dynamics. A new generation of functional gene arrays (GeoChip 3.0) has been developed, with 27,812 probes covering 56,990 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance, and organic contaminant degradation. Those probes were derived from 2,744, 140, and 262 species for bacteria, archaea, and fungi, respectively. GeoChip 3.0 has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating, and the gyrB gene for phylogenetic analysis. Our computational evaluation of probe specificity indicated that all designed probes had a high specificity to their corresponding targets. Also, experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036percent-0.025percent false positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which demonstrated that the structure, composition, and potential activity of soil microbial communities significantly changed with the plant species diversity. All results indicate that GeoChip 3.0 is a high throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning. To our knowledge, GeoChip 3.0 is the most comprehensive microarrays currently available for studying microbial communities associated with geobiochemical cycling, global climate change, bioenergy, agricuture, land use, ecosystem management, environmental cleanup and restoration, bioreactor systems, and human health

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning