The Effect of Homogenization Techniques on the Microheterogeneity of Soil Microbiome Samples - An application of techniques from Incremental Sampling Methodology

Abstract

Soil is one of the most heterogeneous environments in existence, perhaps most notably in the distributional heterogeneity of different soil particles. Shaped by this environment, the soil microbiome shares this characteristic heterogeneity as soil organisms display a very heterogeneous distribution within the soil. This makes it extremely difficult to obtain replicable results from soil samples collected for microbiome research. This has significance for a wide range of fields including agriculture, forestry, medicine, and biobanking. Therefore this study aimed to compare microbiome intra-sample variability after the application of different homogenization procedures. Soil samples from five different fields were collected and separated into three groups. The samples of group 1 were simply aliquoted directly and used as a control. The samples of group 2 were aliquoted after being homogenized with a blender to mix and disaggregate the soil aggregates. The samples of group 3 were homogenized with a blender to mix and disaggregate the soil aggregates followed by using two dimensional Japanese slabcake technique to reduce the effects of stratification during sample size reduction prior to analysis and then aliquoted. Genomic analysis was conducted upon three aliquots of each group and field to identify bacteria and fungi, followed by bioinformatics analysis. Less microheterogeneity was observed between aliquots in group 3 than between aliquots in group 2. Aliquots from both of these treatment groups demonstrated less microheterogeneity than aliquots in the control group, group 1, that were not homogenized at all. Thus, homogenizing soil samples using techniques from the Incremental Sampling Methodology resulted in aliquots from those samples demonstrating less variability in the diversity of the bacterial and fungal taxa present in their microbiome. Homogenizing samples using these specific techniques is superior to using soil samples that are not homogenized or are homogenized using other techniques which do not take the same sources of bias and error into account.

Date of Award	2019
Original language	English
Awarding Institution	Medical University Graz
Supervisor	Berthold Huppertz (Supervisor)