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Supplemental Material
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S1 Statistical analysis of the T-RFLP data
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In order to avoid the incorporation of primer induced signals in the T-RFLP analysis,
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fragments smaller than 50 bp were excluded. An upper fragment length threshold of 560 bp
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was applied to consider also sequences with no restriction site as criterion for the community
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structure (complete amplicon length was 550 bp). Noise removal from the final signal
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measurements, peak binning to account for inter-run differences in T-RF size and
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normalization of signal intensity was conducted according to Abdo et al. (2006) using a cut-
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off value of four times the standard deviation to remove background noise. Multivariate
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statistical analysis of the resulting normalized sample-peak tables were run with the R
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package “vegan” (Oksanen et al., 2006). Non-metric multidimensional scaling (NMDS)
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analyses performed with the Bray-Curtis similarity index (including presence and relative
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abundance of T-RF) iteratively tried to plot the rank order of similarity of communities in a
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way that community point distances are exactly expressed on a two-dimensional sheet
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(greater distances represent greater dissimilarities). The major compositional environmental
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variations were fitted using a linear regression and the ”envfit” algorithm provided with the
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”vegan” package. Significances of single environmental and experimental parameters on the
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NMDS results were tested using the Monte-Carlo permutation test with 1000 permutations
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and final ANOVA. These parameters included incubation time, depth, soil type, litter type,
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alkB gene and mRNA copy number as well as the total alkane amount, the relative amount of
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alkane fractions with different chain-length and the nucleic acid molecule type (for the overall
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analysis the alkB harbouring and expressing communities were combined).
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S2 Significance levels of factors influencing the litter decay in microcosms covered with
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maize or pea litter respectively.
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S3 Relative abundances of terminal restriction fragments (T-RF) in DNA or mRNA samples
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from litter, soil and control compartments detected also in soil and litter isolates. For the
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calculation, all samples in one sampling group (litter; soil; control) were summed with no
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differentiation of litter-, soil type, compartment and incubation time.
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S4 Significance levels of environmental factors correlating with community structure
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changes in alkB harbouring (DNA) or expressing (mRNA) communities (based on NMDS of
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T-RFLP data) in the sandy and the silty soil microcosms incubated with maize or pea straw,
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respectively. In addition, litter communities are also included (maize; pea). Significance
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levels for the overall analysis including T-RFLP analysis of all treatments and layers on alkB
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gene and expression level are given in the last column (all). P values are based on Monte-
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Carlo permutation with 1000 permutations and final ANOVA.
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S5 Relative amount of remaining litter of maize and pea plants after incubation of sandy and
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silty soil microcosms, referred to an initial amount of 1g (dw) of fresh litter material. Error
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bars denote standard deviation (n = 3).
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S6 Community structure cluster analyses of alkB genes (A, B) and transcripts (C, D) in silty
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and sandy soil microcosms covered either with maize (A, C) or pea (B, D) litter as well as in
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the non-litter controls.
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S7 Number of T-RF (i.e. richness) detected in two soil compartments (litter-soil interface,
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bulk soil) after the incubation with maize and pea litter with differentiation of T-RF
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exclusively detected in sand, silt and shared T-RF between both soil types. For reasons of
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simplification no differentiation between the two soil compartments was included.
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S8 T-RF in soil microcosms incubated with maize and pea litter with differentiation of T-RF
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exclusively detected in litter, soil and shared T-RF between litter and soil samples. For
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reasons of simplification no differentiation between the two soil compartments was included.
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S9 T-RFLP based NMDS blot of all alkB gene harbouring and expressing communities of the
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microcosm experiments. Community similarity was calculated using Bray-Curtis similarity
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measurement. Arrows are correlation vectors of community structure differences and
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environmental conditions with significance factors P < 0.1 (for exact significance level see
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S4). Monte-Carlo permutation model based analysis with 1000 permutation and final
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ANOVA was applied to test for significance.
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