Seasonal Fluctuations of Bacterial Community Diversity in Agricultural Soil and Experimental Validation by Laboratory Disturbance Experiments

Abstract

Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to drift apart to inherently different states.

Is the nitrification a redundant process in arid regions?: activity, abundance and diversity of nitrifier microorganisms

“…These results agree with several authors who stated that few microbial population changes along the year (Laverman et al 2001, Meier et al 2008.…”

“…However, these abundance changes did not reach to equalize the magnitude mentioned by other authors (Meier et al 2008). The high nitrifi er abundance in Arid Chaco during wet season has a direct relation to the precipitations recorded during the period, which was twelve fold higher than the accumulated in dr y season (469 vs. 39 mm).…”

Physiological shifts in the microbial community drive changes in enzyme activity in a perennial agroecosystem

“…Letters (lower-case, annual; upper-case, perennial) denote significant differences between sampling dates within an agroecosystem and asterisks denote significant differences between agroecosystems at a sampling date (Tukey's HSD, P \ 0.05) more than twice as much annual root production (Ontl et al 2013) and increases in MBC in response to changes in cropping systems have been documented on similar time scales (1-3 years) (Kallenbach and Grandy 2011). The lack of effect of the perennial cropping system on microbial biomass may be attributable to chronic disturbance associated with intensively managed ecosystems (Allison and Martiny 2008;Dethlefsen and Relman 2011;Meier et al 2007) or the lack of coupling of C and N additions in these systems (Kallenbach and Grandy 2011;Lagomarsino et al 2006). Primary inputs of C (root inputs with high C:N) and N (inorganic fertilizer) were from different sources, which can result in a temporal disconnect in resource availability and subsequent reduction in microbial energy and enzyme efficiency relative to high quality (low C:N) organic sources (Hobbie 2005).…”

Fungal communities are more sensitive indicators to non-extreme soil moisture variations than bacterial communities

“…Climatic models forecast a decrease of average soil moisture and an intensification of extreme events (IPCC, 2007), but it is still uncertain to what extent the soil system can become unbalanced under these perturbations. While many studies have focused on intense water-stress, little attention has been paid to the response of microbial communities in non-extreme conditions to characterise their stability to natural variability (Meier et al, 2008). However, small fluctuations of soil water content in nonextreme conditions represent a common situation that needs to be explored before understanding and deciphering the impact of extreme events.…”