Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples - PubMed (original) (raw)

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

Christian L Lauber et al. FEMS Microbiol Lett. 2010 Jun.

Abstract

Storage conditions are considered to be a critical component of DNA-based microbial community analysis methods. However, whether differences in short-term sample storage conditions impact the assessment of bacterial community composition and diversity requires systematic and quantitative assessment. Therefore, we used barcoded pyrosequencing of bacterial 16S rRNA genes to survey communities, harvested from a variety of habitats [soil, human gut (feces) and human skin] and subsequently stored at 20, 4, -20 and -80 degrees C for 3 and 14 days. Our results indicate that the phylogenetic structure and diversity of communities in individual samples were not significantly influenced by the storage temperature or the duration of storage. Likewise, the relative abundances of most taxa were largely unaffected by temperature even after 14 days of storage. Our results indicate that environmental factors and biases in molecular techniques likely confer greater amounts of variation to microbial communities than do differences in short-term storage conditions, including storage for up to 2 weeks at room temperature. These results suggest that many samples collected and stored under field conditions without refrigeration may be useful for microbial community analyses.

PubMed Disclaimer

Figures

Fig.1

Fig.1

Non-metric Multidimensional Scaling (NMDS) plots of UniFrac weighted and unweighted pairwise distances. Overall community composition was not affected by temperature or duration of storage for weighted UniFrac distances (_P_> 0.1 in all cases). Length of storage significantly affected the skin communities for the unweighted UniFrac metric (P = 0.02). The remaining unweighted UniFrac distances were not significantly different by day or temperature. Blue=sample 1, red = sample 2. Open symbols = Day 3, closed symbols = Day 14. ▲= 20°C, ■ = 4°C, ● = −20°C, ◆ = −80°C.

Fig. 2

Fig. 2

The relative abundance of various bacterial taxa in fecal, skin and soil samples after 14 days of storage. Bars represent the mean abundance of each group at each temperature in descending order (e.g. 20, 4, −20, and −80°C) with 1 standard error of the mean. Abundances of bacterial taxa were classified to family for the fecal samples and to order for the skin and soil samples using the RDPII nomenclature. Differences in relative abundances due to storage temperature were assessed within individual samples using the Kruskall-Wallis test. Asterisk (*) indicates _P_- values < = 0.05.

Similar articles

Cited by

References

    1. Clarke KR, Warwick RM. A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine Ecology-Progress Series. 2001;216:265–278.
    1. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 2005;33:D294–D296. - PMC - PubMed
    1. Costello EK, Lauber CL, Hamady M, Knight R, Fierer N. Bacterial Variation in Human Body Habitats Across Space and Time. Science. 2009;326:1694–1697. - PMC - PubMed
    1. DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006a;34:W394–W399. - PMC - PubMed
    1. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb. 2006b;72:5069–5072. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources