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Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination?

Changey, Frederique and Nunan, Naoise and Herrmann, Anke and Lerch, Thomas Z. (2022). Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination? Ecological Indicators. 139 , 108897
[Research article]

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Abstract

Recent advances in molecular ecology have dramatically improved our knowledge of soil microbial diversity and offers new indicators of soil quality. The usefulness of diversity indices has never been greater as the astronomical amounts of data generated in the literature needs to be synthesized. Despite technical guidelines have been proposed to characterize soil microbiomes using high throughput sequencing, the effect of taxonomic resolution on diversity indices is still largely unknown. Here, we explored how downscaling to higher taxonomic resolution levels may affect alpha-and beta-diversity indices of bacterial communities exposed to different soil organic matter management. To this aim, we collected soil samples in a long-term experimental site (Ultuna, Sweden) where different mineral and organic fertilizers have been applied for since 1956. We used both massive amplicon sequencing from phylum to species (OTU) and molecular fingerprints (PLFA, DGGE and T-RFLP). Our results showed that the discrimination potential increased at finer taxonomic resolution for beta-diversity but not for alpha-diversity indices such as richness and evenness. Also, the relative importance of hierarchical drivers of soil microbial communities such as C, N and pH varied depending on the taxonomic resolution. This study also demonstrated that indicators generated by molecular fingerprints such as PLFA, DGGE and T-RFLP are still consistent to monitor the effect of agricultural management on beta-diversity but not on alpha-diversity, which is useful information as it allows for a better use of results in past literature. We encourage performing such comparative studies on wider surveys, including different contexts and other indicators, in order to increase the efficiency and the robustness of the use of sequencing data in soil biodiversity monitoring.

Authors/Creators:Changey, Frederique and Nunan, Naoise and Herrmann, Anke and Lerch, Thomas Z.
Title:Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination?
Series Name/Journal:Ecological Indicators
Year of publishing :2022
Volume:139
Article number:108897
Number of Pages:11
Publisher:ELSEVIER
ISSN:1470-160X
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Soil Science
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
Keywords:Taxonomic resolution, Microbial communities, Diversity indices, Soil organic matter
URN:NBN:urn:nbn:se:slu:epsilon-p-117324
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-117324
Additional ID:
Type of IDID
DOI10.1016/j.ecolind.2022.108897
Web of Science (WoS)000795711400004
ID Code:28207
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Soil and Environment
(S) > Dept. of Soil and Environment
Deposited By: SLUpub Connector
Deposited On:02 Jun 2022 13:42
Metadata Last Modified:02 Jun 2022 13:51

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