The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

Mariana P Reis,Edmar Chartone-Souza,Francisco A R Barbosa,Marcelo P Ávila,Hendrikus J Laanbroek,Andréa M A Nascimento,Rosalinde M Keijzer

doi:10.3389/fmicb.2015.00898

Abstract

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

Highlights

Nitrification, in which ammonia is converted to nitrite and subsequently to nitrate, is a key process in the global nitrogen cycle that is essential for the functioning of many ecosystems
Principal component analysis, which was based on these five environmental parameters, revealed that the first component (PC1) of the principal component analysis (PCA) biplot, mainly explained the positive correlation of the Carrapatos stream (CS) sample with dissolved oxygen (DO) and Fe, and a negative correlation with NH4+, whereas the opposite was observed for the Tulipa stream (TS) sample
Many studies have revealed that bacterial and archaeal ammoniaoxidizing communities are shaped by different environmental drivers in many ecosystems (Tourna et al, 2008, 2011; Daebeler et al, 2012; Liu et al, 2014)

Summary

Introduction

Nitrification, in which ammonia is converted to nitrite and subsequently to nitrate, is a key process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The first step in nitrification, converts reduced inorganic nitrogen species to oxidized ones (Gruber and Galloway, 2008). Many studies have revealed the dominance of AOA over AOB in many environments (Francis et al, 2005; Leininger et al, 2006; Wuchter et al, 2006; Zhang et al, 2008; Li et al, 2009). AOB seem to be more abundant in metalpolluted environments than AOA (Ruyters et al, 2013; Liu et al, 2014)

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Results

Conclusion