Functional principal component data analysis: a new method for analysing microbial community fingerprints.

A common approach to molecular characterisation of microbial communities in natural environments is the amplification of small subunit (SSU) rRNA genes or genes encoding enzymes essential for a particular ecosystem function. A range of 'fingerprinting' techniques are available for the analysis of amplification products of both types of gene enabling quantitative or semi-quantitative analysis of relative abundances of different community members, and facilitating analysis of communities from large numbers of samples, including replicates. Statistical models that have been applied in this context suffer from a number of unavoidable limitations, including lack of distinction between closely adjacent bands or peaks, particularly when these differ significantly in intensity or size.

Plant host habitat and root exudates shape soil bacterial community structure.

The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under (13)CO(2) (99% of atom (13)C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation.

Rhizosphere bacterial community composition responds to arbuscular mycorrhiza, but not to reductions in microbial activity induced by foliar cutting.

Differences in bacterial community composition (BCC) between bulk and rhizosphere soil and between rhizospheres of different plant species are assumed to be strongly governed by quantitative and qualitative rhizodeposit differences. However, data on the relationship between rhizodeposit amounts and BCC are lacking. Other soil microorganisms, e.

Studying plant-microbe interactions using stable isotope technologies.

Interactions between plants and microorganisms in the rhizosphere are complex and varied. They include the general transfer of nutrients and specific interactions mediated by the release of signalling molecules from plant roots. Until recently, understanding the nature of these interactions was limited by a reliance on traditional, cultivation-based techniques.

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms.

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a 13CO2 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of 13C-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil.