Table 2 Analyzed gene markers and amplicon characteristics

From: Methanol consumption drives the bacterial chloromethane sink in a forest soil

Gene marker

Function

PCR Primer

Sequence (5′-3′)a

Amplicon size (bp)

SNP/ OTUb

Total OTUsc

Labeled OTUsd

Reference

16 S rRNA gene

Ribosomal small subunit RNA

341for

CCTACGGGNGGCWGCAG

464

9

117

5

[60]

785/805rev

GACTACHVGGGTATCTAATCC

[61]

cmuA

chloromethane methyltransferase

cmuAf422

GARGTBGGITAYAAYGGHGG

422

38

8

5

This studyf

cmuAr422

TCRTTGCGCTCRTACATGTCICC

mxaF/xoxF e

methanol dehydrogenase

mdh1

GCGGIWSCAICTGGGGYT

430

39

6

6

This studyf

mdh2

GCGGIWSGAICTGGGGYT

mdhR

GAASGGYTCSYARTCCATGCA

  1. aDegenerate base mixtures: B (C,G,T), H (A,C,T), K (G,T), N (A,C,G,T), R (A,G), S (G,C), Y (C,T), V (A, C, T), W (A,T). Inosine (I) was used instead of the N mixture [62] in some cases
  2. bMaximal Single Nucleotide Polymorphism (SNP) positions possible within an OTU
  3. cCorresponding to the sum of OTUs detected in the 8 microcosms of the SIP experiment. Sequences were affiliated to the same OTU at cutoff values of 98, 90, and 80% sequence identity at the nucleotide level for 16S rRNA gene, cmuA, and mxaF/xoxF amplicons, respectively
  4. dSee Material and Methods for the criteria applied to define OTUs as ‘labeled’
  5. ePrimer pairs allow to amplify both mxaF and xoxF types of methanol dehydrogenase (mdh) sub units Amplifications were performed with two different forward primers (mdh1, mdh2) in order to reduce primer degeneracy and improve PCR efficiency. Amplicons obtained with primers mdh1/mdhR and mdh2/mdhR were pooled before sequencing.
  6. fSee Supplemental Information of Materials and Methods for details
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