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J Microbiol Methods. 2015 Aug;115:112-20. doi: 10.1016/j.mimet.2015.05.027. Epub 2015 Jun 6.

Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils.

Author information

1
H.J. Patterson Hall, Room 1216, Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA. Electronic address: gdlott@umd.edu.
2
Sustainable Agricultural Systems Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA. Electronic address: Jude.Maul@ARS.USDA.GOV.
3
Sustainable Agricultural Systems Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA. Electronic address: Jeffrey.Buyer@ARS.USDA.GOV.
4
H.J. Patterson Hall, Room 1216, Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA. Electronic address: syarwood@umd.edu.

Abstract

We tested a method of estimating the activity of detectable individual bacterial and archaeal OTUs within a community by calculating ratios of absolute 16S rRNA to rDNA copy numbers. We investigated phylogenetically coherent patterns of activity among soil prokaryotes in non-growing soil communities. 'Activity ratios' were calculated for bacteria and archaea in soil sampled from a tropical rainforest and temperate agricultural field and incubated for one year at two levels of moisture availability and with and without carbon additions. Prior to calculating activity ratios, we corrected the relative abundances of OTUs to account for multiple copies of the 16S gene per genome. Although necessary to ensure accurate activity ratios, this correction did not change our interpretation of differences in microbial community composition across treatments. Activity ratios in this study were lower than those previously published (0.0003-210, logarithmic mean=0.24), suggesting significant extracellular DNA preservation. After controlling for the influence of individual incubation jars, significant differences in activity ratios between all members of each phylum were observed. Planctomycetes and Firmicutes had the highest activity ratios and Crenarchaeota had the lowest activity overall. Our results suggest that greater caution should be taken in interpreting soil microbial community data derived from extracted DNA. Indirect extraction methods may be useful in ensuring that microbes identified from extracellular DNA are not erroneously interpreted as components of an active microbial community.

KEYWORDS:

Activity; Oligotrophy; Preservation; eDNA; iDNA

PMID:
26055315
DOI:
10.1016/j.mimet.2015.05.027
[Indexed for MEDLINE]

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