Fig. S1. Heatmap showing microarray results of pmoA amplicons retrieved from various soils using the A682r reverse primer. Microarray signals were normalized against the mean of overall array intensity and against reference values determined for each probe individually (Bodrossy et al., 2003; Lüke et al., 2011). Relative fractions were calculated. Probes used for statistical analyses are highlighted in blue. A phylogenetic tree depicting an overview of the probe phylogeny as well as the rational for the probe selection is described in Lüke and colleagues (2011). Sample sites are described in Table S1.


Fig. S2. Cluster analysis of standardized T-RFLP data obtained from Indonesian paddy soils. The heatmap shows the relative abundance of individual T-RFs obtained using the pmoA reverse primers mb661 (A) and A682r (B). Affiliation of T-RFs: 33 bp – AOB, MO3 cluster, type Ib, pxmA – 36 bp – type Ib – 46 bp – AOB – 58 bp – pxmA – 79 bp – type Ib, RPC-2, pxmA – 114 bp – AOB, pmoA-2, pxmA – 203 bp – unknown – 208 bp – type Ia – 226 bp – type Ib – 241 bp – type Ia – 244 bp – Methylosinus/Methylocystic type II – 349 bp – type Ia, pmoA-2–377 bp – type Ia – 437 bp – type Ia, pmoA-2, pxmA – 505 bp – type Ia.


Fig. S3. Unrooted neighbour joining tree showing the phylogentic relationship of clusters defined by DBSCAN in Fig. 4. In contrast to Fig. 5, all sequences have been used for tree construction. Colour coding for individual clusters is identical to Fig. 4.


Fig. S4. Non-metric multidimensional scaling (NMDS) with three axes based Jukes-Cantor corrected pmoA nucleotide sequence distances. The data set and ordination are identical to Fig. 4, but here, sequences are colour-coded based on their soil origin. To reduce overplotting, a transparency of 0.5 was used.


Fig. S5. Mosaic plot showing the relative importance of clusters defined in Fig. 4. Data set and colour-coding are identical to Fig. 4.


Table S1. Description of sampling sites. The Indonesian site selected for additional pmoA amplicon pyrosequencing is highlighted in red. Fully developed paddy soils are called Anthrosols according to the international soil classification system (IUSS Working Group WRB, 2007). The parent soils that have developed naturally on the Indonesian and Chinese sites before having been altered by paddy use are Fluvisols, Vertisols, Ferralsols/Acrisols and Andosols/Umbrisols. The Fluvisols in Cixi (China) consist of silt-rich marine sediments and were brought to terrestrial soil formation by human land reclamation. Vertisols (Java) are clay-rich soils, and the clay fraction is dominated by strongly swelling and shrinking clays leading to the formation of strong and large aggregates. In Ferralsols and Acrisols (Sumatra), the clay fraction consists mainly of kaolinites allowing only small nutrient reserves and a weak macroaggregation. Andosols (Java and Sumatra) develop from volcanic ashes, are very loose and rich in organic matter and Fe oxides. Some soils from volcanic ashes do not entirely meet the Andosol criteria and have to be classified as Umbrisols.


Supplementary file 1 (pyro_typeII_dna). High-quality subset of the pmoA pyrosequencing data obtained from various paddy soils. These sequences were used for the analysis of type II methanotrophs depicted in Figs 4–6 and Figs S3–S5. The data set was created by importing all raw sequences into ARB, removing all sequences shorter than 400 bp and manually checking sequences for frame shifts. Only good quality sequences longer than 399 bp and without frame shifts were maintained. These sequences were classified by calculation of neighbour joining trees and only sequences related to the Methylosinus/Methylocystis group were selected.


Supplementary file 2 (pyro_typeII_dna.nds). Sequence associated information (metadata) referring to the data set in supplementary file 1.

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