title: Molecular phylogeny of heterotrophic nitrifiers and aerobic denitrifiers and their potential role in ammonium removal.
abstract: To investigate the physiology and taxonomic composition of the key players of nitrification and denitrification processes in paddy fields, culture dependent and independent studies have been carried out. A total of 28 bacterial strains have been screened in which six were capable of reducing nitrate and nitrite as well as having significant ammonium removal potential. 16S rRNA-PCR-DGGE-based molecular typing of enriched batch culture was done with time duration to explore and identify dominant and stable soil denitrifiers. Notably, three isolates namely PDN3, PDN19, PDN14 were found to be efficiently involved in the removal of 70.32, 71.46, and 81.50% of NH4 (+) and showed closest similarity (>98%) with Bacillus cereus, Bacillus subtilis, and Pseudomonas aeruginosa strains, respectively. The bacterial strain PDN14 showed maximum growth with highest ammonium removal rate (2.78 gN/(m(3) ·h) has also been characterized based on nosZ gene which showed similarity to uncultured γ- Proteobacteria, P. aeruginosa sp. B3. Median joining (MJ) network and rRNA secondary structure have been analyzed for their detailed taxonomic diversity and derived haplotype-based co-occurrence. Results demonstrated that such strains can serve as good candidate for in situ nitrogen transformation in paddy soils and improvingly characterized by physiological and detailed phylogenetic approaches.
authors.affiliation: Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India.
authors.forename: Meenakshi
authors.initials: M
authors.lastname: Srivastava
authors.affiliation: Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India.
authors.forename: Manish Singh
authors.initials: MS
authors.lastname: Kaushik
authors.affiliation: Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India.
authors.forename: Anumeha
authors.initials: A
authors.lastname: Singh
authors.affiliation: Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India.
authors.forename: Deepti
authors.initials: D
authors.lastname: Singh
authors.affiliation: Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India.
authors.forename: Arun Kumar
authors.initials: AK
authors.lastname: Mishra
mesh_terms: D064751:Ammonium Compounds / Q000378:metabolism*; D001419:Bacteria / Q000302:isolation & purification / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D001673:Biodegradation, Environmental; D058440:Denitrification / Q000502:physiology*; D052836:Heterotrophic Processes; D009566:Nitrates / Q000378:metabolism*; D058465:Nitrification / Q000502:physiology*; D009573:Nitrites / Q000378:metabolism*; D012275:Oryza; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D062065:Wastewater / Q000737:chemistry
chemical_list: D064751:Ammonium Compounds; D009566:Nitrates; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D062065:Wastewater
keywords: Aerobic denitrification; Haplotype network; Heterotrophic nitrification; PCR-DGGE; Phylogeny; rRNA secondary structure