Figure 2: Transcript profiles of methanotrophs in paddy soil with and without high-affinity methane oxidation activity.

(a) Methane oxidation and carbon assimilation pathways of methanotrophs that were detected in high-affinity methane oxidation (HAMO) and non-HAMO paddy soils. Gene transcript abundance was normalized as the reads number per 2 million annotated transcripts. The numbers in red and blue indicate the abundance of transcripts detected in HAMO and non-HAMO soil transcriptomes, respectively. The enzymes encoded by these genes are as follows: acsA, acetoacetyl-CoA synthetase; atoB, acetyl-CoA acetyltransferase; bdh, 3-hydroxybutyrate dehydrogenase; eda, 2-dehydro-3-deoxyphosphogluconate aldolase; edd, phosphogluconate dehydratase; eno, enolase; fad, 3-hydroxyacyl-CoA dehydrogenase; fae, formaldehyde-activating enzyme; fbaA, fructose-bisphosphate aldolase; fch, methenyltetrahydrofolate cyclohydrolase; fdh, formate dehydrogenase; fhcABCD, formylmethanofuran dehydrogenase; ftfL, formate-tetrahydrofolate ligase; gap, glyceraldehyde-3-phosphate dehydrogenase; gk, D-glycerate 2-kinase; glyA, serine hydroxymethyltransferase; gnd, 6-phosphogluconate dehydrogenase; gpmI, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; hbd, 3-hydroxybutyryl-CoA dehydrogenase; hprA, hydroxypyruvate reductase; hps, 3-hexulose-6-phosphate synthase; mch, methenyltetrahydromethanopterin cyclohydrolase; mcl, Malyl-CoA lyase; mmo, methane monooxygenase (soluble); mtdA, methylenetetrahydrofolate dehydrogenase; mtdB, methylene-tetrahydromethanopterin dehydrogenase; mxaF, methanol dehydrogenase; pfk, 6-phosphofructokinase; pgi, glucose-6-phosphate isomerase; pgl, 6-phosphogluconolactonase; pgk, phosphoglycerate kinase; phaZ, poly(3-hydroxybutyrate) depolymerase; phbB, acetoacetyl-CoA reductase; phbC, poly-beta-hydroxybutyrate polymerase; phi, 6-phospho-3-hexuloisomerase; pmo, methane monooxygenase (particulate); pyk, pyruvate kinase; sga, serine-glyoxylate transaminase; zwf, glucose-6-phosphate-dehydrogenase. Dotted arrows represent multiple enzymatic reactions. 1,3-BPG, 1,3-bisphosphoglycerate; EMP pathway, Embden–Meyerhof–Parnas pathway; F-1,6-BP, fructose 1,6-bisphosphate; GAP, glyceraldehyde-3-phosphate; G6P, glucose-6-phosphate; KDPG, 2-keto-3-deoxy-6-phosphogluconate; MOB, methane-oxidizing bacteria; PEP, phosphoenolpyruvate; 2-PG, 2-phosphoglycerate; 3-PG, 3-phosphoglycerate; 6PG, 6-phosphogluconate; 6PGL, 6-phospho-glucono-1,5-lactone; PHB, poly-beta-hydroxybutyrate; H₄F, tetrahydrofolate; H₄MPT, tetrahydromethanopterin. (b) Transcript abundance of the pmoA lineages in the HAMO and non-HAMO metatranscriptomes. Transcript abundance of each pmoA lineage was normalized as the read number per 2 million annotated transcripts. (c) The phylogeny of the detected pmoA2 transcript (red). The tree was constructed using MEGA 4.0 based on 125 derived amino-acid sequences. Representatives of the pmoA2 OTUs were obtained from pmoA gene amplicon pyrosequencing (blue) and pmoA2 gene clone library sequencing (green), and representatives of the three pyrosequenced pmoA1 lineages (violet) are also shown. Bootstrap values >50% (1,000 replicates) are shown at the nodes. The scale bar represents 5% sequence divergence.