TY - JOUR
T1 - Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity
AU - Tzeneva, Vesela A.
AU - Salles, Joana F.
AU - Naumova, Natalia
AU - de Vos, Willem M.
AU - Kuikman, Peter J.
AU - Dolfing, Jan
AU - Smidt, Hauke
N1 - Funding Information:
This work was supported by a grant from the European Communities EC project “Exploration of Genomic and Metabolite Diversity of a Novel Group of Abundant Soil Bacteria” (BACREX-project QLK3-2000-01678). The work of N. Naumova was partly funded by the International Agricultural Center (Wageningen, The Netherlands) and by the SBRAS Integration Grant 24 (Novosibirsk, Russia). We especially acknowledge Antoon Akkermans, who sadly passed away in 2006, for critical reading and stimulating discussions. We thank Paul Poulton, Rothamsted experimental station, and the Soil Science Center of Wageningen University and Research Center for kindly providing soil samples.
Copyright:
Copyright 2009 Elsevier B.V., All rights reserved.
PY - 2009/3
Y1 - 2009/3
N2 - Archived soil samples are a valuable source for retrospective ecological studies, and their recent analysis using molecular ecological approaches has drawn significant attention within the scientific community. However, the possibility of addressing ecological questions regarding detectable microbiota in dried and extensively stored soils has not yet been fully evaluated. To achieve this, soil samples collected from two long-term grassland experiments in the United Kingdom and The Netherlands were subjected to air-drying at 40-42 °C and stored at room temperature. Total bacterial, Bacillus benzoevorans-related and eukaryotic communities associated with these samples were analyzed by DGGE-fingerprinting of PCR-amplified ribosomal RNA gene fragments. Changes in microbial community structure due to drying and storage were evaluated by multivariate analysis in relation to changes caused by other environmental conditions, such as soil pH, type of fertilizer and vegetation. Soil drying and storage affected the detectable community structure, but did not materially impair our capacity to identify the effect of soil parameters studied in long-term grassland experiments. Although, in some cases, the amplitude of the influence of a given parameter changed due to sample preservation, analyses revealed that pH, fertilization and soil type significantly influenced microbial community structure in the analyzed samples.
AB - Archived soil samples are a valuable source for retrospective ecological studies, and their recent analysis using molecular ecological approaches has drawn significant attention within the scientific community. However, the possibility of addressing ecological questions regarding detectable microbiota in dried and extensively stored soils has not yet been fully evaluated. To achieve this, soil samples collected from two long-term grassland experiments in the United Kingdom and The Netherlands were subjected to air-drying at 40-42 °C and stored at room temperature. Total bacterial, Bacillus benzoevorans-related and eukaryotic communities associated with these samples were analyzed by DGGE-fingerprinting of PCR-amplified ribosomal RNA gene fragments. Changes in microbial community structure due to drying and storage were evaluated by multivariate analysis in relation to changes caused by other environmental conditions, such as soil pH, type of fertilizer and vegetation. Soil drying and storage affected the detectable community structure, but did not materially impair our capacity to identify the effect of soil parameters studied in long-term grassland experiments. Although, in some cases, the amplitude of the influence of a given parameter changed due to sample preservation, analyses revealed that pH, fertilization and soil type significantly influenced microbial community structure in the analyzed samples.
KW - Bacillus benzoevorans-relatives
KW - DGGE
KW - Eukarya
KW - Soil bacteria
KW - Soil sample preservation
UR - http://www.scopus.com/inward/record.url?scp=61449237181&partnerID=8YFLogxK
U2 - 10.1016/j.resmic.2008.12.001
DO - 10.1016/j.resmic.2008.12.001
M3 - Article
C2 - 19111612
AN - SCOPUS:61449237181
SN - 0923-2508
VL - 160
SP - 89
EP - 98
JO - Research in Microbiology
JF - Research in Microbiology
IS - 2
ER -