Temporal dynamics of soil microbial communities over hourly, daily and seasonal scales
Recently advances have been made in understanding the factors governing the composition of soil microbial communities, however major knowledge gaps remain. In particular, relatively little is known about how the composition of soil microbial communities varies over time and across a narrow pH gradient (e.g. < 1 pH unit). To address this question we collected soil samples from a 2.4 x 2.4m plot in a deciduous forest in western Maryland on hourly, daily and seasonal scales. Samples were collected on 2 - 3 different dates during winter, spring, summer and fall of 2010. On each date, four replicate samples were removed every four hours during a 24 hour period, yielding a total of 24 samples per day (240 samples in total). We tested the hypothesis that soil bacterial community composition shifts diurnally during the growing season due to expected diurnal changes in temperature and root exudates. Bacterial community composition was assessed using 454 sequencing of 16S amplicons. Faith’s Phylogenetic Diversity (FD, a measure of alpha diversity) was quantified and we characterized ß-diversity with non-metric multidimensional scaling analysis using the Unifrac Metric (a measure of phylogenetic overlap).
We found a clear seasonal effect with respect to alpha and ß-diversity. Average alpha-diversity based on FD ranged from a low of 47.4 during fall to a high of 54.2 during spring. Non-metric multidimensional scaling revealed that soil bacterial community composition during fall was distinct from winter and spring, when bacterial community composition were similar. Soil pH ranged between 4.17 and 4.82 and was not associated with shifts in bacterial community composition. Alpha and ß-diversity varied from hour to hour and day to day, but there was no clear pattern in the variation of bacterial community composition on a diurnal basis during any season. These findings suggest that litter quality and/or quantity may be driving the observed seasonal patterns in the composition of bacterial communities: the fresh input of litter that occurs during autumn may select for a distinct soil microbial community. If so, an understanding of soil carbon dynamics - particularly the role of litter quality and quantity - may help to predict variation in the structure and function of soil microbial communities through time.