Table 1.
Verification of shotgun isotope array detection by SIP
| Probe name | Hybridization resulta | Closest match in databases | Gene feature(s) or encoded protein | E-value | % similarity (no. of identical nucleotides/total no. of nucleotides) | Assimilation of tracer compound in SIPc |
|---|---|---|---|---|---|---|
| probe-04 | p | Thauera sp. MZ1T, complete genome | 2-Isopropylmalate synthase | 0 | 82.5 (611/741) | + |
| probe-07 | p | Acidovorax sp. JS42, complete genome | Transposase, IS4 family protein | 1.0E−137 | 78.0 (499/640) | + |
| probe-12 | p | Methylococcus capsulatus strain Bath, complete genome | Glutathione S-transferase domain protein | 1.0E−09 | 66.9 (192/287) | − |
| probe-16 | p | Polaromonas naphthalenivorans CJ2, complete genome | RNA polymerase, sigma-24 subunit, ECF subfamily | 2.0E−109 | 80.1 (370/462) | + |
| probe-18 | p | Polaromonas naphthalenivorans CJ2 plasmid pPNAP05, complete sequence | NAb | 0 | 81.5 (567/696) | + |
| probe-36 | n | Plasmodium knowlesi strain H | DNA repair protein RAD50 | 6.2E−01 | 96.3 (26/27) | − |
| probe-49 | n | Azoarcus sp. BH72, complete genome | Penicillin-binding protein | 2.2E+00 | 96.2 (25/26) | − |
| probe-59 | n | Paracoccus denitrificans PD1222 chromosome 2, complete sequence | hydrogenase-1 expression HyaE | 1.0E−59 | 69.0 (460/667) | + |
| probe-86 | n | Pedobacter heparinus DSM 2366, complete genome | Na+/H+ antiporter | 2.2E+00 | 90.3 (28/31) | − |
a
In [14C]acetate hybridization. p, positive; n, negative.
b
NA, not available.
c
Data indicate whether an increase in copy numbers in high-density fractions was observed (+, observed; −, not observed).