Article Figures & Data
Figures
- Fig. 1.
Vertical profiles of in situ CH4 mixing ratios in forest soil in winter (January 1999) (A) and in summer (July 1999) (B).
- Fig. 2.
Vertical profiles of CH4 oxidation rates per gram of fresh soil (A) and soil water content (B) in winter and summer. The CH4 oxidation rates in winter are from single measurements, whereas those in summer are means of triplicates (coefficient of variation = 4 to 22%).
- Fig. 3.
Vertical profiles of the total extractable DNA content per gram of dry soil (A) and the pmoA concentration of the PCR products from each soil section (B) in winter and summer. In winter, DNA was analyzed only between 0 and 16 cm deep; nopmoA was detected between 0 and 6 cm deep.
- Fig. 4.
(A) DGGE pattern obtained with the universal SSU rDNA primer set. (B) Phylogenetic tree constructed with partial 16S rDNA sequences of the marked DGGE bands from the forest soil core sampled in winter. The phylogenetic tree shows the relationships of the marked DGGE bands to members of the domain Bacteria. The scale bar indicates the estimated number of base changes per nucleotide sequence position; the following 16S rDNA sequences (accession numbers) were taken from data banks: ms6, ms10, and ms14 are clones from a peat bog retrieved with primers specific for methanotrophs (AF111789, AF111787, and AF111788); strain LR1 is a high-affinity type II methanotroph (Y18442); strain K is an acidophilic methanotroph (Y17144).
- Fig. 5.
DGGE pattern obtained with the pmoA primer set targeting the gene of the α subunit of particulate methane monooxygenase in winter (A) and in summer (B). The arrow shows the direction of increasing denaturant and electric field. Bands MR1 to MR5 were sequenced; band 6 was not sequenced.
- Fig. 6.
Phylogenetic tree based on the derived amino acid sequences of pmoA and amoA fragments, showing the relation of the pmoA sequences (MR1 to MR5) retrieved from forest soil to pmoA and amoA sequences of other methanotrophs and ammonium oxidizers. Bands of the same electrophoretic mobility were repeatedly sequenced from different DGGE gels and lanes (soil depths) to prove sequence identity. Sequences were labeled according to the DGGE band position (MR1 to MR5), the season of sampling (W, winter; S, summer), and the soil depth (in centimeters). The scale bar indicates the estimated number of changes per amino acid sequence position. The pmoA sequences Rold, Maine, and RA are novel pmoA sequences retrieved from forest soils (23); LR1 is a high-affinity type II methanotroph (Y18443); and HB is a thermophilic methanotroph (U89302).
