Article Figures & Data
Figures
- Fig. 1.
14C-PLFA fingerprints for MOB. (A) Unknown methanotrophs that metabolized atmospheric methane in two forest soils in Denmark (Rold) and the United States (Maine). (B) Type I methanotroph Methylomicrobium album BG8 and type II methanotroph Methylosinus trichosporium OB3b. Each bar represents the amount of radiolabel in a fraction as a percentage of the radioactivity in all fractions. The following reference standard PLFAs coeluted with the 14C-PLFAs: 14:0, i15:1, and a15:1 in fraction 2; 16:1w9 and 16:1w8 in fraction 4; 16:1w7, 16:1w5, and 16:0 in fraction 5; i17:0, a17:0, and 17:1w8 in fraction 7; and 18:1w9, 18:1w8, and 18:1w7 in fraction 11.
- Fig. 2.
Alignment of predicted peptide sequences of PmoA and AmoA from representative methanotrophic and nitrifying bacteria with soil clone RA14 and RA21 sequences. Residues which are universally conserved in extant MOB are highlighted with black. Putative MMO signatures are highlighted with dots, and putative AMO signatures are highlighted with grey. The horizontal lines indicate predicted hydrophilic domains conserved in all of the peptides (15). The sequences shown (and their accession numbers) are as follows: Ms.tri, Methylosinus trichosporium (U31650); Mc. M,Methylocystis sp. strain M (U81596); Mc.par,Methylocystis parvus (U31651); Nc.oce, Nitrosococcus oceanus (U31652); Mb.alb, Methylomicrobium album BG8 (U31654); Mm.met, Methylomonas methanica S1 (U31653); LK6,Methylocaldum tepidum LK6 (U89304); Mc.cap,Methylococcus capsulatus Bath (L40804); Nm.eur,Nitrosomonas europaea (L08050); Nl.mul, Nitrosolobus multiformis (U31649); AHB1, Nitrosospira sp. strain AHB1 (X90821); Nspira, Nitrosospira sp. strain Np22 (U31655).
- Fig. 3.
Unrooted phylogenetic trees showing relationships of RA14 and RA21 to representative methanotrophs and ammonia-oxidizing bacteria. (A) Tree constructed by using a 171-amino-acid segment of the 27-kDa subunit of MMO (PmoA or AmoA). (B) Tree constructed by using a restricted sequence alignment (125 amino acids) in which putative signature residues (see Fig. 2) were omitted from the analysis. On the basis of the bacterial phylogeny derived from rRNA (10, 26,42), the root of the trees is predicted to lie on the branch indicated by a dot. The numbers at the nodes indicate the numbers of times the groups occurred in 100 bootstrap replicates. ApproximateKm values for CH4(Km CH4) of the holoenzymes are indicated as micromolar concentrations (Table 1). For the sequence accession numbers see the legend to Fig. 2. Abbreviations: Mb,Methylomicrobium; Mm., Methylomonas; Nc.,Nitrosococcus; Mc., Methylocystis; Ms.,Methylosinus; Nm., Nitrosomonas; Nl.,Nitrosolobus; Nspira, Nitrosospira.
- Fig. 4.
Phylogenetic analysis of the derived amino acid sequences encoded by the pmoA genes of methanotrophs, nitrifiers, and Rold, Maine, and Pantanal soil DNA samples. The dendrogram shows the results of an analysis in which PROTDIST was used. Bootstrap values greater than 50% derived from 100 replicates are also shown. The bar represents 10% sequence divergence, as determined by measuring the lengths of the horizontal lines connecting any two species.
Tables
- Table 1.
Some characteristics of AAOB (nitrifying bacteria), methanotrophic bacteria, and unknown high-affinity methane oxidizers in soila
Bacteria Phylogenetic affiliation Membrane type Major fatty acidsb Key enzyme Apparent Km for CH4 (μM)c Vmax for CH4 (mmol · g of cells−1· h−1) Oxidation inhibited by C2H2, C2H4, DME, and COd Growth inhibited by elevated NH3 concn CH4 required to maintain activity % Assimilation of oxidized CH4e MAB Group 1 γ-Proteobacteria Stacked, central 14:0, 16:0, and 16:1 species pMMO (+ some sMMO) 0.8–32 10–31 + + + 29–62 Group 2 α-Proteobacteria Flat, peripheral 18:1 species pMMO (+ some sMMO) 0.8–32 10–31 + + + 29–62 Soil high affinity ? ? 18:1 species ? 0.01–0.06 ? + + + 20–54 AAOB Group 3 β-Proteobacteria Flat, peripheral 16:0 and 16:1 species AMO 2,000 0.03–0.59 + − − 0–17 Group 4 γ-Proteobacteria Stacked, central 16:0 and 16:1 species AMO 6.6 0.01–0.08 + − − 1–47 ↵a Data from references 1, 2, 5,9, 12, 17, 19, 20, 22, 28, 30, 31, 39, and40.
↵b A major fatty acid is present at a concentration of >10% in at least one member of each group.
↵c The values for nitrifiers were based on theKi of CH4 for ammonia oxidation.
↵d DME, dimethyl ether.
↵e The fate of labelled methane in nitrifiers is not known. The apparent assimilation could be due to nonspecific labelling by formaldehyde or assimilation at the level of CO2.
