The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys.

Catarina M Magalhã£Es,S Craig Cary,Ana Machado,Bã©Atrice Frank-Fahle,Charles K Lee

doi:10.3389/fmicb.2014.00515

Abstract

The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.

Highlights

Nitrification represents the oxidative part of the nitrogen (N) cycle and refers to the two-step process where ammonia is oxidized to nitrite and subsequently to nitrate
In Antarctic coastal mineral soils, 99% of the detected 16S rRNA sequences were affiliated with Thaumarchaeota (Ayton et al, 2010), as did more than 80% of all archaeal sequences identified in the McMurdo Dry Valleys (Richter et al, 2014)
The amoA gene copy numbers for the Dry Valleys are significantly higher than those reported for soils from the Antarctic Peninsula (Jung et al, 2011). This may be due to the fact that we developed and optimized a new set of Quantitative PCR (qPCR) primers for archaeal and bacterial amoA genes found in the Dry Valleys, whereas the qPCR primers used by Jung et al (2011) were based on existing primer sets developed for very different environments (Rotthauwe et al, 1997; Okano et al, 2004; Francis et al, 2005; de la Torre et al, 2008)

Summary

INTRODUCTION

Nitrification represents the oxidative part of the nitrogen (N) cycle and refers to the two-step process where ammonia is oxidized to nitrite and subsequently to nitrate. Recent studies reporting limited diversity and abundance of Archaea in the Dry Valleys have identified a consistently high proportion of sequences (80–99%) affiliated with Thaumarchaeota (formerly known as Crenarchaeota Marine Group 1.1b; Ayton et al, 2010; Richter et al, 2014). These findings represent cursory evidence for archaeal nitrification in the Dry Valleys. The previous study reported a high degree of physicochemical heterogeneity and distinct bacterial communities, likely driven by the disparate physicochemical conditions We hypothesized that such physicochemical heterogeneities exert similar selective effects on AOA and AOB amoA genes distribution and abundance

MATERIALS AND METHODS

RESULTS AND DISCUSSION

Findings

CONCLUSION