Open AccessAlkane‐degrading bacteria at the soil–litter interface: comparing isolates with T ‐ RFLP ‐based community profiles
Author(s) -
Giebler Julia,
Wick Lukas Y.,
Chatzinotas Antonis,
Harms Hauke
Publication year - 2013
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/1574-6941.12097
Subject(s) - biology , microcosm , alkane , litter , soil microbiology , 16s ribosomal rna , plant litter , bacteria , alkb , microorganism , microbiology and biotechnology , ecology , ecosystem , soil water , gene , escherichia coli , genetics , biochemistry , catalysis
Alkane‐degrading bacteria were isolated from uncontaminated soil microcosms, which had been incubated with maize litter as natural alkane source. The isolates served to understand spatio‐temporal community changes at the soil–litter interface, which had been detected using alkB as a functional marker gene for bacterial alkane degraders. To obtain a large spectrum of isolates, liquid subcultivation was combined with a matrix‐assisted enrichment ( T eflon membranes, litter). Elevated cell numbers of alkane degraders were detected by most probable number counting indicating enhanced alkane degradation potential in soil in response to litter treatment. Partial 16 S r RNA gene sequencing of 395 isolates revealed forty different phylogenetic groups [operational taxonomic units ( OTU s)] and spatio‐temporal shifts in community composition. Ten OTU s comprised so far unknown alkane degraders, and five OTU s represented putative new bacterial genera. The combination of enrichment methods yielded a higher diversity of isolates than liquid subcultivation alone. Comparison of 16 S r RNA gene T ‐ RFLP profiles indicated that many alkane degraders present in the enrichments were not detectable in the DNA extracts from soil microcosms. These possibly rare specialists might represent a seed bank for the alkane degradation capacity in uncontaminated soil. This relevant ecosystem function can be fostered by the formation of the soil–litter interface.