The phylogeny of the genus Azohydromonas supports its transfer to the family Comamonadaceae

References

1. Yousuf B, Kumar R, Mishra A, Jha B. Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach. FEMS Microbiol Lett 2014; 360:117–125 [View Article] [PubMed]
   [Google Scholar]
2. Coelho MRR, de Vos M, Carneiro NP, Marriel IE, Paiva E et al. Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer. FEMS Microbiol Lett 2008; 279:15–22 [View Article] [PubMed]
   [Google Scholar]
3. Song Y, Li Y, Zhang W, Wang F, Bian Y et al. Novel biochar-plant tandem approach for remediating hexachlorobenzene contaminated soils: proof-of-concept and new insight into the rhizosphere. J Agric Food Chem 2016; 64:5464–5471 [View Article] [PubMed]
   [Google Scholar]
4. Peña C, Castillo T, García A, Millán M, Segura D. Biotechnological strategies to improve production of microbial poly-(3-hydroxybutyrate): a review of recent research work. Microb Biotechnol 2014; 7:278–293 [View Article] [PubMed]
   [Google Scholar]
5. Gahlawat G, Srivastava AK. Estimation of fundamental kinetic parameters of polyhydroxybutyrate fermentation process of Azohydromonas australica using statistical approach of media optimization. Appl Biochem Biotechnol 2012; 168:1051–1064 [View Article] [PubMed]
   [Google Scholar]
6. Xie CH, Yokota A. Reclassification of Alcaligenes latus strains IAM 12599^T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol 2005; 55:2419–2425 [View Article]
   [Google Scholar]
7. Nguyen TM, Kim J. Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in south korea. Journal of Microbiology 2017; 55:330–336
   [Google Scholar]
8. Dahal RH, Chaudhary DK, Kim D-U, Kim J. Azohydromonas caseinilytica sp. nov., a nitrogen-fixing bacterium isolated from forest soil by using optimized culture method. Front Microbiol 2021; 12:647132 [View Article] [PubMed]
   [Google Scholar]
9. Xue H, Piao C-G, Bian D-R, Guo M-W, Li Y. Azohydromonas aeria sp. nov., isolated from air. J Microbiol 2020; 58:543–549 [View Article] [PubMed]
   [Google Scholar]
10. Palleroni NJ, Palleroni AV. Alcaligenes latus, a new species of hydrogen-utilizing bacteria. Int J Syst Bacteriol 1978; 28:416–424 [View Article]
    [Google Scholar]
11. Willems A, Gillis M, De Ley J. Transfer of Rhodocyclus gelatinosus to Rubrivivax gelatinosus gen. nov., comb. nov., and phylogenetic relationships with Leptothrix, Sphaerotilus natans, Pseudomonas saccharophila, and Alcaligenes latus. Int J Syst Bacteriol 1991; 41:65–73 [View Article]
    [Google Scholar]
12. Willems A, Gillis M. Comamonadaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria Wiley; 2015 pp 1–6
    [Google Scholar]
13. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
14. Vesth T, Lagesen K, Acar Ö, Ussery D. CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One 2013; 8:e60120 [View Article] [PubMed]
    [Google Scholar]
15. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
    [Google Scholar]
16. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
    [Google Scholar]
17. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
18. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
19. Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 2018; 46:W282–W288 [View Article] [PubMed]
    [Google Scholar]
20. Nei M, Kumar S. Molecular Evolution and Phylogenetics, 1st ed. New York: Oxford University Press; 2000
    [Google Scholar]
21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
22. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]