Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae

Question

[Nafi]

Acinetobacter guillouiae has been reported to possess nitrogen-fixing genes (DOI: 10.1007/s40011-020-01168-0). However, I was unable to identify any nif genes (nifH, nifB, nifE, etc.) or nitrogenase proteins in the genomic data available on the NCBI website (https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=106649). Could I be overlooking something?

[GenoMax]

Have you considered the possibility that if no strains of Acinetobacter guillouiae available in NCBI show presence of nitrogen fixing genes then the original report (including the strain identification) may be incorrect.

Using nifH or nitrogenase protein sequences for searches against nr seems to bring up similarities to ParA/ApbC family of proteins in Acinetobacter guillouiae (taxid:106649).

A quick LLM search seems to indicate that these proteins belong to the P-loop NTPase superfamily, meaning they share structural features related to ATP binding and hydrolysis, such as Walker A and B motifs (LTRVVFNQKGGVGKSSITVNLAAISAYQGFKTLVIDLDPQANSSQYLL is what shows up on BLAST search) but they do not share functional protein domains.

Answer 1

[Mensur Dlakic]

The specific strain described in that paper (Acinetobacter guillouiae EU-B2RT.R1) doesn't seem to be available in NCBI. It could be as simple as that. Did you test all 46 strains that can be found at NCBI for these genes?

[Nafi]

Yes, I have tested all of them. I guess NCBI does not have this particular strain.