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. 2024 Oct 18;10(21):e39436.
doi: 10.1016/j.heliyon.2024.e39436. eCollection 2024 Nov 15.

Genomic insights into heterotrophic nitrifying-aerobic denitrifying bacteria from petroleum terminal effluents

Lutecia Rigueira Medina  1 , Lívia Carneiro Fidélis Silva  1 , Helena Santiago Lima  1 , Pedro Marcus Pereira Vidigal  2 , Alex Gazolla de Castro  1 , Maira de Paula Sousa  3 , Rodrigo Suhett de Souza  3 , Sérgio Oliveira de Paula  4 , Cynthia Canêdo da Silva  1
Affiliations

Genomic insights into heterotrophic nitrifying-aerobic denitrifying bacteria from petroleum terminal effluents

Lutecia Rigueira Medina et al. Heliyon. .

Abstract

Heterotrophic nitrification-aerobic denitrification (HN/AD) is a single-organism process that converts ammonia into nitrogen gas under strictly aerobic conditions, playing a crucial role in biological ammonia removal from industrial wastewater. Despite several studies, significant knowledge gaps remain about the genes involved in the process. This study aimed to characterize the genomes of four HN/AD bacterial strains, Pseudomonas stutzeri UFV5, Pseudomonas balearica UFV3, Rhodococcus ruber UFV2, and Gordonia amicalis UFV4, and identify potential genes involved in the HN/AD process. Results revealed that shared genes of these strains were primarily involved in amino acid and protein biosynthesis. The two Pseudomonas strains had more genes linked to nitrogen metabolism than the others. Additionally, four strains showed a significant number of hypothetical proteins and genes related to oxidative stress. Notably, no common nitrogen metabolism genes were found among the strains, indicating a lack of a shared HN/AD pathway. However, comparing these genomes with previous transcriptomic data of the P. stutzeri UFV5 identified nine shared proteins as potential HN/AD pathway candidates. This study enhances our understanding of the genomes of these HN/AD-capable bacterial strains and identifies nine candidate genes as markers for the HN/AD process.

Keywords: Comparative genomic analysis; Differential expressed genes; HN-AD; Nitrogen removal.

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Conflict of interest statement

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Lutecia Rigueira Medina reports financial support was provided by Minas Gerais State Foundation of Support to the Research. Cynthia Canedo da Silva reports a relationship with Petrobras that includes: funding grants. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Image 1
Graphical abstract
Fig. 1
Fig. 1
Subsystem annotation by Rapid Annotation using Subsystem Technology (RAST). The graph shows the categories of subsystems of protein-coding genes. The number of genes assigned to each functional category is represented in parentheses. A) Pseudomonas stutzeri UFV5, B) Pseudomonas balearica UFV3, C) Rhodococcus rubber UFV2, e D) Gordonia amicalis UFV4.
Fig. 2
Fig. 2
Representation of OrthoVenn3 analysis results among the four HN/AD strains. (A) Visual representation of cluster sharing and unique clusters among the strains. (B) Graphical visualization of orthology cluster analysis results among the four strains and the number of proteins (reduce the Venn diagram size).
Fig. 3
Fig. 3
Comparative genomics of HN/AD strains against genes involved in conventional anaerobic denitrification. According to KEGG: Pseudomonas stutzeri UFV5 (A) and Pseudomonas balearica UFV3 (B), The genes filled with (formula image) were found in the HN/AD strain of this study.
See this image and copyright information in PMC

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