Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1016/j.ejsobi.2014.10.006
Title (Primary) Evaluating T-RFLP protocols to sensitively analyze the genetic diversity and community changes of soil alkane degrading bacteria
Author Giebler, J.; Wick, L.Y.; Harms, H.; Chatzinotas, A.
Source Titel European Journal of Soil Biology
Year 2014
Department UMB; iDiv
Volume 65
Page From 107
Page To 113
Language englisch
Keywords alkB T-RFLP; 16S rRNA T-RFLP; Protocol evaluation; Soil bacterial communities; Restriction enzyme selection; Alkane degradation
UFZ wide themes RU3;
Abstract Due to the enormous complexity of soil bacterial communities, functional gene markers, like the alkB gene coding for the bacterial alkane monooxygenase, might be more suitable to monitor specific ecosystem functions, i.e. alkane degradation, compared to phylogenetic gene markers which include species not providing the respective service. However, the routine application of such functional fingerprints needs careful method development and evaluation. This study aimed at identifying a reliable, highly resolving fingerprinting method to monitor alkane degrading communities in soil. Therefore, we (i) evaluated various available terminal restriction fragment length polymorphism (T-RFLP) protocols for the alkB gene, (ii) comparatively analyzed the same soil communities targeting either a functional (alkB) or a phylogenetic marker gene (16S rRNA gene) in the T-RFLP, and (iii) judged on the applicability of diversity indices to follow diversity changes in the degrader community during alkane input. In silico restriction of 83 alkB gene sequences from public databases identified HpyCH4V as the enzyme yielding the highest T-RF richness for alkB. Analyzing DNA extracts from microcosms of two different agricultural soils (sandy and silty, amended with either maize or pea litter as alkane source) revealed a higher sensitivity of the alkB T-RFLP compared to 16S rRNA gene T-RFLP for following spatiotemporal changes in the alkane degrader community. As expected, the diversity indices based on either phylogenetic or functional fingerprinting profiles deviated significantly, but both resulted in lower richness estimates compared to an alkane degrading enrichment culture obtained from the same soil samples. The latter indicated that alkane degradation is a very common capability of soil bacteria. However, as the two fingerprinting methods monitor different kinds of diversity, they might provide complementary answers (i.e. phylogenetic and functional) to the same research questions, i.e. which is the robustness of an ecosystem function in a given system.
Persistent UFZ Identifier
Giebler, J., Wick, L.Y., Harms, H., Chatzinotas, A. (2014):
Evaluating T-RFLP protocols to sensitively analyze the genetic diversity and community changes of soil alkane degrading bacteria
Eur. J. Soil Biol. 65 , 107 - 113 10.1016/j.ejsobi.2014.10.006