Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

Abstract

bIt is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.

Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? A demonstration in oilseed rape

“…Our results confirm the statement of Yan et al . () that the dilution method is effective in obtaining a decreasing gradient in microbial OTUs richness, but that it allows no accurate predictions on the community structure and genera abundances. Soil bacterial richness has been shown to be of poor importance for mechanisms such as degradation of carbon sources or nitrogen cycling, since bacterial species are probably redundant in ecosystem functioning (see Roger et al ., for an overview of the bacterial diversity‐ecosystem functioning literature including the dilution approach).…”

Higher fungal diversity is correlated with lower CO2emissions from dead wood in a natural forest: BioRxiv preprint

“…The one exception, Valentin et al 26 , found a positive relationship, but in that study, field-collected microbial communities were serially diluted and re-inoculated into laboratory wood incubations. Serial dilution does not necessarily remove microbial species, but it does make all species less abundant 27 , which might have reduced decomposition rates. In contrast, field studies to date have reported only ambiguous relationships between fungal diversity and decomposition rates.…”

Assessment of the petroleum hydrocarbon biodegradation potential of the sediment microbial community from an urban fringing tidal marsh of Northern New England

“…which is expected given that dilution alone reduces diversity (Franklin et al, 2001, Hewson et al, 2003 Schaffer et al, 2000, Yan et al, 2015). Comparing the diversity values obtained after one day of 400 treatment (we were not able to compare diversity values at 10 days of treatment due to the low read 401 number in the 10-day no alkane control), and the 10 day cultures, indicated that exposure to gasoline and 402 n-hexane reduced diversity to a greater degree than seen in the dodecane treatment or the no alkane 403 further study would be required to determine if the sediment microbial community of the fringing marsh 410…”