Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition

Blaud, A.; Menon, M.; van der Zaan, B.; Lair, G.J.; Banwart, S.A.

Abstract

Soil aggregates are microhabitats for microorganisms, and directly influence microorganisms that live within and are influenced by microorganisms in return. Two methods are used to isolate soil aggregates by their size: dry sieving (sieving air-dried soil) and wet sieving (sieving soil in water). Wet-sieving methods are generally considered to represent separation of aggregate classes that are stable to physical disaggregation in water, a condition considered favorable for protecting soil structure over time. However, little is known about the effect of sieving methods on microbial abundance, diversity, and functions, hindering the understanding of the relationship between soil structure and soil aggregates as habitat and soil microorganisms. In this study, the effect of dry and wet sieving on bacterial diversity, and abundance of microorganisms involved in N fixation (nifH gene), nitrification (amoA bacteria and archaea), and denitrification (narG, nirS and nosZ genes), was determined for four sizes of soil aggregates from a cropland and grassland. Quantitative-PCR (Q-PCR) showed little differences in relative gene abundance between size fractions of soil aggregates, but wet-sieving method significantly increased gene abundance for amoA bacteria, nirS and nosZ genes. When the N functional genes were expressed as percentage of the bacterial 16S rRNA genes, the wet sieving resulted in significantly higher genes percentage for all the genes (except for narG gene), and significant differences between soil aggregate size fractions at the grassland site. The different sieving methods resulted in different bacterial community compositions, but only the wet-sieving method was able to reveal significant differences in bacterial community composition between soil fractions in grassland. The results demonstrate significantly different quantitative and qualitative interpretation of soil microbial community depending on whether aggregate samples were obtained from wet or dry sieving, highlighting the importance in the choice of the sieving method.

Citation

Blaud, A., Menon, M., van der Zaan, B., Lair, G., & Banwart, S. (2017). Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition. In D. Sparks, & S. Banwart (Eds.), Quantifying and Managing Soil Functions in Earth's Critical Zone - Combining Experimentation and Mathematical Modelling (119-142). Academic Press. https://doi.org/10.1016/bs.agron.2016.10.006

• Acceptance Date: Nov 9, 2016
• Online Publication Date: Dec 29, 2016
• Publication Date: 2017
• Deposit Date: Nov 30, 2018
• Publicly Available Date: Dec 4, 2018
• Publisher: Academic Press
• Pages: 119-142
• Series Title: Advances in Agronomy
• Series Number: 142
• Series ISSN: 0065-2113
• Book Title: Quantifying and Managing Soil Functions in Earth's Critical Zone - Combining Experimentation and Mathematical Modelling
• Chapter Number: 5
• ISBN: 9780128122228
• DOI: https://doi.org/10.1016/bs.agron.2016.10.006
• Keywords: Quantitative-PCR,Amplicon sequencing,Nitrogen fixation, Nitrification, Denitrification, Soil aggregates, Grassland, Cropland,
• Public URL: http://researchrepository.napier.ac.uk/Output/1348414
• Publisher URL: https://www.sciencedirect.com/science/article/pii/S0065211316301122