Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies

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Lindström , S , Rowe , O , Timonen , S , Sundström , L & Johansson , H 2018 , ' Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies ' , PeerJ , vol. 6 , 5289 . https://doi.org/10.7717/peerj.5289

Title: Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies
Author: Lindström, Stafva; Rowe, Owen; Timonen, Sari; Sundström, Liselotte; Johansson, Helena
Contributor organization: Organismal and Evolutionary Biology Research Programme
Evolution, Sociality & Behaviour
Biosciences
Tvärminne Zoological Station
Sari Timonen / Research Group
Department of Microbiology
Doctoral Programme in Microbiology and Biotechnology
Doctoral Programme in Wildlife Biology
Teachers' Academy
Date: 2018-07-20
Language: eng
Number of pages: 24
Belongs to series: PeerJ
ISSN: 2167-8359
DOI: https://doi.org/10.7717/peerj.5289
URI: http://hdl.handle.net/10138/239796
Abstract: Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.
Subject: NGS
T-RFLP
Fungi
Bacteria
Ants
Formica exsecta
Illumina MiSeq
Spatiotemporal trends
Microbial communities
1181 Ecology, evolutionary biology
1183 Plant biology, microbiology, virology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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