Temporal and land use effects on soil bacterial community structure of the machair, an EU Habitats Directive Annex I low-input agricultural system

• Soil compartment and temporal factors were the main drivers of bacterial community structure.
• Land use was a sub-dominant significant factor in determining bacterial communities.
• Bacterial communities correlated with soil moisture content, but not any other physico-chemical property.
• Bacterial community field studies should take temporal variability into account.

The machair, a low-input agricultural system in the extreme north-west of Scotland, is a rare example of an extant system that has never been intensively cultivated. The bacterial community structure represents an opportunity to test variation connected with temporal, soil compartment and land use factors. To achieve this objective a two-year, three season sampling regime over the three major land uses present: cropped, fallow and grasslands was performed. Bacterial communities of rhizosphere and bulk soil compartments were assessed using terminal restriction fragment length polymorphism (T-RFLP). Machair bacterial community structure was primarily determined by soil compartment and temporal factors, with differences both between and within years highly significant. Although land use was not the main determinant of bacterial community, clear differences were detected. Cropped and fallow sites contained a similar bacterial community while grassland sites were different. Correlation with soil physico-chemical factors indicated that machair bacterial community structure may be driven to some degree by soil moisture content.This study highlights the need to take seasonal and annual variation into account when assessing bacterial communities in an agricultural setting.