Air-Drying, Cooling and Freezing for Soil Sample Storage Affects the Activity and the Microbial Communities from Two Mediterranean Soils

Abstract

The selection of soil storage conditions must take into account the diversity of soils and their environmental characteristics, because different soil types may vary in their physical and chemical characteristics and microbial populations. As a result, identical storage conditions can produce different effects on different soil samples, and understanding the influence of soil storage in respect to the microbial community is essential for further microbial research. In this study, two different characteristics were used to assess the influence of soil processing and storage on two Mediterranean soils: respiratory activity and bacterial community composition in relation to three common storage conditions: air-drying, cooling and freezing. Samples from both soils (a Calcaric Regosol and a Haplic Arenosol) were air-dried or stored at either 4°C or −20°C for 12 months, and a PCR-DGGE analysis was performed to reveal changes in the whole bacterial community, and more specifically in the Firmicutes group, throughout the storage period. After storage, aliquots of the soil samples were incubated for 28 days at 25°C to assess changes in microbial activity, using respirometry, and molecular methods were used to determine the differences in the microbial community composition during the respirometric incubation. Results clearly show that any storage condition affects the microbial community and its activity, and this effect increases with the vulnerability of the soil. The study also reveals the need of incubating the soil samples to allow active bacteria to reach sufficiently high population sizes to be detected, as the non-incubated samples have not shown any change. The soil microbial community has been found to be adapted to its particular environmental conditions. In that sense, results suggest that Firmicutes may have a more common occurrence in the soil that is usually dried, since these bacteria can be more resistant to drying due to their spore-forming strategy. The stored samples undergo significant increases (45 to 70%, generally speaking) in the Cumulative Respiration, mainly in the most aggressive treatments (drying and freezing) whereas Basal and Substrate Induced Respiration rates tend to decrease (30 to 45%, depending on the soil and treatment), and the Respiratory Activation Quotient remains lower or unaltered, indicating low stress levels. The different physical, chemical and biological properties of the two soils lead to different suitable storage requirements, although all of them produce alterations in the studied parameters. Considering the results from microbial communities and activity, for the Calcaric Regosol, freezing could be the most suitable method, while for the Haplic Arenosol, it would be more appropriate to use air-drying.

Keywords:

• soil storage
• respirometry
• PCR-DGGE
• soil bacteria
• Mediterranean soil
• community structure
• molecular ecology
• biomineralization

Acknowledgments

This work was supported by the Spanish Government, Project REN 2003-09513-C02-01. We are very thankful to Dr. Lluís Bañeras (University of Girona) and to the anonymous reviewers for their interesting and appropriate comments on the manuscript.