Bacterial Domination Over Archaea in Ammonia Oxidation in a Monsoon-Driven Tropical Estuary

Abstract

Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

“…Although, to the best of our knowledge, the effect of daily salinity fluctuations has not been tested directly, some previous works point that AOM communities from downstream estuarine systems displayed similar potential nitrification rates under salinities ranges of 15 and 30 psu (Magalhaes et al, 2005;Bernhard et al, 2007;Santos et al, 2018). Yet, it should be noted that within the AOM, AOB and AOA activity may differ in response to different salinities, as previously reported in other high salinity amplitude environments such as Weeks Bay (Caffrey et al, 2007), Douro River estuary (Magalhães et al, 2009), Plum Island Sound estuary (Bernhard et al, 2007(Bernhard et al, , 2010, Huntington Beach subterranean estuary (Santoro et al, 2008), Cochin estuary (Puthiya Veettil et al, 2015), and Colne estuary (Li et al, 2015).…”

Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas

“…For example, AOA were more abundant than AOB in the North Sea, the Sargasso Sea and the Northern South China Sea (Dang et al, 2013 ; Newell et al, 2013 ; Lipsewers et al, 2014 ); a positive correlation between AOA abundance and ammonia-oxidation rates has been observed. However, the abundance of AOA was decoupled from nitrification in the Central California Current (Santoro et al, 2010 ), and AOB was dominant in the Colne Estuary, the Cochin Estuary, and the South Atlantic Ocean (Xu et al, 2014 ; Li et al, 2015 ; Veettil et al, 2015 ). The relative importance of AOA and AOB in marine nitrogen cycle is therefore still under debate.…”

The Distribution of Fecal Contamination in an Urbanized Tropical Lake and Incidence of Acute Diarrheal Disease

“…The E. coli were enumerated using the quantitative real-time polymerase chain reaction (qPCR) technique. The water sample (1 L) was filtered through a polycarbonate membrane filter with a pore size of 0.2 μm, and DNA was extracted following the method in ref with small modifications as described in our previous publication . Absolute qPCR was carried out in a Roche Lightcycler 96-well Real-time PCR system (Roche, USA) to enumerate the number of E. coli present in the water column.…”

“…The water sample (1 L) was filtered through a polycarbonate membrane filter with a pore size of 0.2 μm, and DNA was extracted following the method in ref 38 with small modifications as described in our previous publication. 39 Absolute qPCR was carried out in a Roche Lightcycler 96-well Real-time PCR system (Roche, USA) to enumerate the number of E. coli present in the water column. The recombinant plasmid (pJET; 2974bp) containing a portion of β-D-glucuronidase gene (187 bp) was linearized using restriction enzyme NcoI and used as the standard.…”