Influence of depth and sampling time on bacterial community structure in an upland grassland soil

Abstract

Temporal and spatial variation of soil bacterial communities was evaluated with both molecular and metabolic profiling techniques. Soil cores (20 cm deep) were taken from an upland grassland in the Scottish Borders (UK) over 3 days in July 1999, and on single days in October 1999, April 2000, and August 2000. Cores were separated into four 5-cm depths to examine vertical spatial distribution. The 0^5-, 5^10-and 10^15-cm samples represented organic horizons whilst the 15^20-cm depths were from a mineral horizon. The potential metabolic activities were analysed using BIOLOG-GN plates, whereas genotypic diversity was evaluated using molecular profiling of amplified 16S rRNA and 16S rDNA gene fragments (denaturing gradient gel electrophoresis (DGGE)). BIOLOG-GN analysis revealed decreased substrate utilisation in the lowest depths, which was coupled with changes in the DNA and RNA DGGE profiles. Seasonal variation was pronounced in the 5^10-cm and 10^15-cm organic horizons for the July samplings whilst the 15^20-cm depths appeared more stable. Potential factors influencing the observed changes in bacterial communities resulting from soil depth and sampling time are discussed.

Assessing the Potential of Bacterial DNA Profiling for Forensic Soil Comparisons*

“…Horswell et al (4) found that although samples collected from the same site 8 months apart were less similar to each other than those collected in a very short time frame, they still showed a high degree of similarity (70% compared with 90%). Although seasonal and temporal variations in soil microbial DNA profiles need to be investigated further, these previous studies (4,20,21) and the preliminary results from the current study would support the potential of the ecosystem‐discrimination‐based approach to compare forensic soil samples. Stable soil microbial DNA profiles may allow comparisons to be made between soil on, for example, a suspect's shoe and a possible crime scene despite significant time lapses between the collection of samples.…”

“…However, they will all still be present in the soil and thus will be detected by DNA profiling methods (such as those used in the current study) that examine the entire soil bacterial community rather than only the active members. Griffiths et al (21) examined the same soils in the four different seasons, and found that only the samples collected in the summer were significantly different from those collected in all the other seasons (which were not significantly different from each other). Horswell et al (4) found that although samples collected from the same site 8 months apart were less similar to each other than those collected in a very short time frame, they still showed a high degree of similarity (70% compared with 90%).…”

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218O

“…; Griffiths et al. ).The data from our study suggested that the semantide utilized played more of a role in the recovered richness and diversity than their indicators of biological activity (labeled nucleic acid). The Morisita‐Horn analysis clearly showed the two DNA libraries and two RNA libraries were highly similar to one another (HDNA ≈ TDNA, HRNA ≈ TRNA), and the DGGE analysis supported the sequencing‐based data.…”

The degradation of the herbicide bromoxynil and its impact on bacterial diversity in a top soil

“…The lane background was subtracted by using a rolling disc algorithm and the lanes were ‘normalized’ to ensure all lanes contained the same amount of total signal. Lane profiles were corrected for differences in migration rate by manually assigning R f lines to marker lane bands (Griffiths et al. 2003).…”