Genome Sequence of a Highly Efficient Aerobic Denitrifying Bacterium, Pseudomonas stutzeri T13

Abstract

Pseudomonas stutzeri T13 is a highly efficient aerobic denitrifying bacterium. Information about the genome of this aerobic denitrifying bacterium has been limited until now. We present the draft genome of P. stutzeri T13. The results could provide further insight into the aerobic denitrification mechanism in strain T13.

GENOME ANNOUNCEMENT

Aerobic denitrification is a novel biological process of nitrogen removal from nitrate by its conversion to nitrogen gas under aerobic conditions (3). Aerobic denitrifying bacteria, which include Thiosphaera pantotropha, Alcaligenes faecalis, Pseudomonas putida, Pseudomonas stutzeri, and so on (4), can simultaneously utilize oxygen and nitrate as electron acceptors. P. stutzeri T13 is a Gram-negative, rod-shaped, aerobic denitrifying bacterium isolated from activated sludge from a municipal wastewater treatment plant. The rates of nitrate and total nitrogen removal by strain T13 could reach 97.75% and 89.74%, respectively. However, the genes related to aerobic denitrification in strain T13 were not determined. In order to determine the related genes and mechanism of aerobic denitrification of P. stutzeri T13, its genome has been sequenced.

The genome of strain T13 was sequenced using the Illumina High-Seq 2000 system. The reads were de novo assembled by using Velvet 1.2.03 (6), and this generated 71 large contigs (>300 bp). The N50 of contig length is 16 kb, and the largest contig assembled is approximately 541.2 kb. The draft sequence is 4,650,137 bases in length, with a G+C content of 63.9%. The genome was annotated using the RAST annotation server (1) and the NCBI Prokaryotic Genome Annotation Pipeline (5). A total of 4,335 coding sequences and 48 structural RNAs were identified. There are 392 subsystems in the genome, as determined by the RAST server (1). Comparison with the genome sequences available at the RAST server suggested that the closest neighbor of strain T13 is P. stutzeri A1501 (score, 527), followed by Azotobacter vinelandii DJ (score, 425) and Pseudomonas fluorescens Pf-5 (score, 409).

In the genome of strain T13, we found a total of 32 genes related to nitrogen removal. Of these genes, 10 related to nitrate reductase were located on the genome of strain T13, especially including 3 genes encoding the periplasmic nitrate reductase. As previously reported, the periplasmic nitrate reductase plays an important role in the aerobic denitrification process (2). Seven nitrite reductase-encoding genes were found in this genome, and the gene encoding ammonia monooxygenase was also present. There were also four genes encoding nitrate/nitrite transporters and seven genes encoding nitrate ABC transporters in the genome of strain T13. Furthermore, we also determined some genes encoding a nitrate/nitrite response regulator protein, a nitrate/nitrite sensor protein, and a fumarate and nitrate reduction regulatory protein. The results suggest that strain T13 contains the complete aerobic denitrification metabolic pathway and provide a good foundation for further research.

Nucleotide sequence accession numbers.

The P. stutzeri strain T13 whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. ALJB00000000. The version described in this paper is the first version, ALJB01000000.