TABLE 2.
Summary of taxonomic classification of draft genomes
| Draft genome | Classification of essential single-copy genes by MEGANa | Inference from phylogenic tree of conserved marker genesb | Classification of 16S rRNA sequences using RDP Classifierc | Top BLASTN hits to NCBI 16S rRNA database | Top BLASTN hit to clone libraries of Blöthe and Roden (6) |
|---|---|---|---|---|---|
| Gallionellaceae sp. (KS-Tueb) | Gallionellaceae | Gallionellaceae | Sideroxydans | 96% to Sideroxydans lithotrophicus ES-1, 94% to Gallionella capsiferriformans ES-2, 94% to Gallionella sp. strain SCGC AAA018-N21 | 100% to clone F30F68 (OTU1) |
| Gallionellaceae sp. (KS-Mad) | Gallionellaceae | Gallionellaceae | Sideroxydans | 95–96% to S. lithotrophicus ES-1, 94% to G. capsiferriformans ES-2, 94% to Gallionella sp. SCGC AAA018-N21 | 100% to clone F30F68 (OTU1), 100% to clone F29F67 (OTU1) |
| Bradyrhizobium sp. | Bradyrhizobium | Bradyrhizobium | Bradyrhizobium | 99% to Bradyrhizobium valentinum LmjM3, 99% to Bradyrhizobium jicamae PAC68, 99% to Bradyrhizobium pachyrhizi PAC48 | 89% to Parvibaculum sp. strain MBNA2 (OTU3) |
| Comamonadaceae sp. | Comamonadaceae | Comamonadaceae | Comamonas | 97% to Comamonas badia IAM 14839, 95% to Comamonas nitrativorans 23310, 94% to Alicycliphilus denitrificans BC | 95% to Comamonas sp. strain MPI12 (OTU2) |
| Rhizobium composite bin | Rhizobium/Agrobacterium group | Rhizobium/Agrobacterium group | Rhizobium | 98% to Rhizobium rosettiformans W3, 98% to Rhizobium daejeonense L61, 97% to Agrobacterium fabrum C58 | 90% to Parvibaculum sp. MBNA2 (OTU3) |
| Rhodanobacter sp. | Rhodanobacter | Rhodanobacter | Rhodanobacter | 99% to Rhodanobacter denitrificans 2APBS1, 99% to Rhodanobacter thiooxydans LCS2, 98% to Rhodanobacter caeni MJ01 | 100% to Rhodanobacter sp. strain MBNA3 (OTU4) |
a
Classification is based on MEGAN lowest common ancestor using BLASTP search of essential single-copy genes (see Fig. S1 in the supplemental material).
b
Classification is based on the phylogenetic tree constructed using conserved phylogenetic marker genes (see Fig. S3 in the supplemental material).
c
Classification is from Ribosomal Database Project (RDP) (http://rdp.cme.msu.edu/) Classifier, with a confidence level of 80%.