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

  • Environmental Microbiology
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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 × 105 cells ml−1) > γ-proteobacteria (0.9 to 4.6 × 104 cells ml−1) > anammox (0.49 to 1.9 × 104 cells ml−1) > AOA (0.56 to 6.3 × 103 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.

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Acknowledgments

The authors thank the Director, National Institute of Oceanography, Goa and the Scientist-in-charge, NIO, RC-Kochi for extending all necessary support. They express their gratitude to Dr. C.T. Achuthankutty, Visiting Scientist, National Centre for Antarctic and Ocean Research, Goa, for critically reading the manuscript and improving its presentation. The authors thank the reviewers for their insightful comments which improved the scientific content. Vpv is thankful for the fellowship given by COMAPS –ICMAM project. JC is a recipient of DST WoS-A fellowship. This work was done using MMRF facility and is duly acknowledged.

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Authors and Affiliations

  1. Council of Scientific and Industrial Research (CSIR), National Institute of Oceanography (NIO), Dona Paula, Goa, 403004, India

    Shanta Nair

  2. Regional Centre, CSIR - National Institute of Oceanography, Cochin, Kerala, 682018, India

    Vipindas Puthiya Veettil, Anas Abdulaziz, Jasmin Chekidhenkuzhiyil, Lallu Kalanthingal Ramkollath, Fausia Karayadi Hamza, Balachandran Kizhakkepat Kalam & Muraleedharan Kallungal Ravunnikutty

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  1. Vipindas Puthiya Veettil
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  2. Anas Abdulaziz
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Correspondence to Anas Abdulaziz.

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Supplementary Table 1

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Supplementary Fig. 1

Representative images of samples hybridized with FISH probes for eubacteria (a), archaea (b), ammonia oxidizing β-proteobacteria (c) and Nitrosococcus (d) (PPTX 661 kb)

Supplementary Fig. 2

Representative images of DGGE pattern of ammonia oxidizing β-proteobacteria (A) and archaeal ammonia monoxygenase (amoA) (B) in surface (s) and bottom (b) samples of sampling stations (PPTX 700 kb)

Supplementary Fig. 3

Abundance of Nitrospira (a) and Nitrobacter (b) in the surface (blue bars) and bottom (red bars) waters from five sampling stations in the Cochin estuary. (PPTX 199 kb)

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Puthiya Veettil, V., Abdulaziz, A., Chekidhenkuzhiyil, J. et al. Bacterial Domination Over Archaea in Ammonia Oxidation in a Monsoon-Driven Tropical Estuary. Microb Ecol 69, 544–553 (2015). https://doi.org/10.1007/s00248-014-0519-x

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