Investigating the impact of storage conditions on microbial community composition in soil samples.
Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.
Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA. brubin@fieldmuseum.org
Benjamin E R
BE
Rubin
Sean M
SM
Gibbons
Suzanne
S
Kennedy
Jarrad
J
Hampton-Marcell
Sarah
S
Owens
Jack A
JA
Gilbert
D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development*; D044822:Biodiversity; D003080:Cold Temperature; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D017753:Ecosystem; D005615:Freezing; D006863:Hydrogen-Ion Concentration; D064307:Microbiota / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology; D013997:Time Factors
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012987:Soil