Introduction to Establish the Comparative Analysis of 16S rRNA Gene Sequences with amoA and nxrA for Nitrifying Bacteria Isolated from East Kolkata Wetland: an International Ramsar Site

Abstract

The nitrogen cycle is most complex and very important for the life on earth. Nitrifying bacteria which carried out nitrogen cycling process play a vital role in water quality control, thus creating a genomic fingerprint database for surveillance and monitoring of genetic variability of nitrifying bacteria is very important and also to establish a Biosecurity protocol for the Bheries located in different areas of West Bengal. The currently evolutionary relationships and the natural diversity of Ammonia Oxidizing Bacteria (AOB) and Nitrite Oxidizing Bacteria (NOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA) and Nitrite oxidoreductase (NxrA) in the East Kolkata Wetland. This study extended significantly the 16S rRNA and amoA databases for AOB, nxrA databases for NOB. Therefore, either of the functional markers (amoA or nxrA) can be used to trace ammonia oxidizers or structural marker (16S rDNA) can be used to trace specific species in environmental studies. These techniques included the use of 16S rDNA genes to characterize natural AOB and NOB populations and to analyze their taxonomic and phylogenetic features. The current perception of AOB and NOB phylogeny established by comparative 16S rRNA sequence analysis could be confirmed independently by exploiting the gene amoA and nxrA genes and proved as an alternative phylogenetic marker. The aim of our work is to investigate the potential of the ammonia monooxygenase subunit A gene (amoA) and Nitrite oxidoreductase (nxrA) gene as functional markers for AOBs and NOBs along with 16S rDNA sequence analysis in EKW. For ecological surveillance, genes like amoA and nxrA specific for the nitrifying bacteria under present research work could be a more reliable tool.

Water quality assessment of East Kolkata Wetland with a special focus on bioremediation by nitrifying bacteria

“…; KF618623, KF618626, KF618624, and KF618625 for Nitrosomonas sp.) was previously published and reported (Saha et al 2014). Further confirmation was carried out through amoA and nxrA functional gene analysis.…”

“…Cultures were initially identified by gram staining. Suspected cultures were evaluated for presence of ammonia and nitrite and vice versa for production of nitrite and nitrate (Saha et al 2014;Roalkvam et al 2020). Identification of Nitrosomonas was tested by the Nessler's reagent (Raud et al 2013;Agus Fitri et al 2017) and Nitrosomonas and Nitrobacter were confirmed through Trommsdrof's reagent (Hanks & Weintraub 1936;Kshatri et al 2017).…”

“…and 4 Nitrosomonas sp. isolates were characterized through the 16SrRNA PCR technique (Saha et al 2014), and gene sequences were analysed and submitted to the NCBI-GenBank (accession numbers: KF618620, KF618621, and KF618622 for Nitrobacter sp. ; KF618623, KF618626, KF618624, and KF618625 for Nitrosomonas sp.).…”

“…The important physicochemical parameters of water such as temperature, pH, dissolved oxygen (DO), total dissolved solids (TDS), Biological oxygen demand (BOD), Chemical oxygen demand (COD), nitrate-nitrogen (NO 3 -N), ammonia-nitrogen (NH 3 -N) and phosphate-phosphorous (PO À3 4 ) need to be assessed properly in different seasons for fish-health management. EKW not only serves as a rich source of nutrients but also harbours efficient and commercially important bacteria, such as nitrifying bacteria and heavy metal utilizing bacteria and microbes, that act as bioremediators by assimilating nitrogen and producing extracellular enzymes (Ghosh et al 2007;Saha et al 2013Saha et al , 2014Sahaya Sukeetha et al 2019).…”

Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe

“…In contrast, the present study is consciously limited to the bacterial ammonia oxidizers (AOB) which are considered to belong to the most thoroughly investigated nitrifiers 15 . Furthermore, they can be regarded as one of the few cases in microbial ecology where pure cultures of nearly all recognized lineages of descent are available 16 . With the exception of the halophilic Nitrosococcus species [17][18][19][20] and the recently proposed Candidatus Nitrosoglobus terrae isolated from acidic soils 19 all AOB belong to the family Nitrosomonadaceae 21 within the (recently proposed to be obsolete 22 ) class Betaproteobacteria.…”