Sample storage for soil enzyme activity and bacterial community profiles.
Storage of samples is often an unavoidable step in environmental data collection, since available analytical capacity seldom permits immediate processing of large sample sets needed for representative data. In microbiological soil studies, sample pretreatments may have a strong influence on measurement results, and thus careful consideration is required in the selection of storage conditions. The aim of this study was to investigate the suitability of prolonged (up to 16 weeks) frozen or air-dried storage for divergent soil materials. The samples selected to this study were mineral soil (clay loam) from an agricultural field, humus from a pine forest and compost from a municipal sewage sludge composting field. The measured microbiological parameters included functional profiling with ten different hydrolysing enzyme activities determined by artificial fluorogenic substrates, and structural profiling with bacterial 16S rDNA community fingerprints by amplicon length heterogeneity analysis (LH-PCR). Storage of samples affected the observed fluorescence intensity of the enzyme assay's fluorophor standards dissolved in soil suspension. The impact was highly dependent on the soil matrix and storage method, making it important to use separate standardisation for each combination of matrix type, storage method and time. Freezing proved to be a better storage method than air-drying for all the matrices and enzyme activities studied. The effect of freezing on the enzyme activities was small (<20%) in clay loam and forest humus and moderate (generally 20-30%) in compost. The most dramatic decreases (>50%) in activity were observed in compost after air-drying. The bacterial LH-PCR community fingerprints were unaffected by frozen storage in all matrices. The effect of storage treatments was tested using a new statistical method based on showing similarity rather than difference of results.
Wallenius
K
K
University of Helsinki, Department of Food and Environmental Sciences, PO Box 56, FI-00014 University of Helsinki, Finland. kaisa.wallenius@helsinki.fi
Rita
H
H
Simpanen
S
S
Mikkonen
A
A
Niemi
R M
RM
D001419:Bacteria / Q000145:classification / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics* / Q000302:isolation & purification; D003890:Desiccation; D004798:Enzymes / Q000235:genetics* / Q000302:isolation & purification; D005615:Freezing; D056186:Metagenomics / Q000379:methods*; D012988:Soil Microbiology; D013048:Specimen Handling / Q000379:methods*
D001426:Bacterial Proteins; D004798:Enzymes