Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China

Abstract

The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on amoA gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA amoA gene copy numbers ranged from 9.6 × 106 to 5.1 × 107 copies per gram of sediment and AOB amoA gene ranged from 9.5 × 104 to 6.2 × 105 copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-011-3107-8) contains supplementary material, which is available to authorized users.

Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

“…Diversity estimators of the clone libraries in this study were within the same range previously reported at other environmental ecosystems (16,19,20,21,56,57). Also, AOB generally had a lower diversity of amoA genes than did AOA in the intertidal sediments of the Yangtze Estuary, which was consistent with the results from other estuarine and coastal environments (16,19,20,21).…”

“…In contrast to previous reports that AOA were more abundant than AOB in both terrestrial and marine systems (19,22,24,32,65), our qPCR results indicated that bacterial amoA gene copies were more numerous (1.1 to 47.1 times) than archaeal amoA gene copies in most of the sampling habitats. This was consistent with the results in the Weeks Bay estuary and the San Francisco Bay estuary, where the AOB amoA copy numbers were also greater than AOA amoA copy numbers at most of the sampling sites (14,20).…”

“…In marine environments, AOA have been assumed to be more important contributors to ammonia oxidation than bacteria, based on molecular and biogeochemical data (29,30). In contrast, in estuarine ecosystems, their relative importance in ammonia oxidation remains more ambiguous and uncertain (19,20,31,32), which may imply a more complex interaction between dynamics of ammonia oxidizers and associated activity in these environments. Due to effects of land-sea interaction, estuaries and adjacent areas often experience tidal changes, salinity intrusions, and nutrient pulses, which may have important impacts on shaping dynamics of ammonia oxidizers.…”

“…However, this view was challenged by the discovery of genes encoding proteins with homology to ammonia monooxygenases (amoA) in genome fragments of archaea which are affiliated with the phylum Thaumarchaeota (11,12,13). Since ammonia-oxidizing archaea (AOA) were discovered, they have been detected in various environments, including soils and sediments (12,14,15,16,17), estuaries (11,18,19,20), subterranean environments (21), oxic and suboxic marine layers (22,23,24), sponges (25), corals (26), and wastewater sludge (27). So far, most studies have shown that a large proportion of the Thaumarchaeota are autotrophic and capable of performing the oxidation of ammonia to nitrite (15,22), although several studies reported that some of these archaea may also be able to assimilate organic compounds, like amino acids (13,28).…”

Shifts of archaeal community structure in soil along an elevation gradient in a reservoir water level fluctuation zone

“…The distribution of archaeal assemblages was affected by both biotic and abiotic factors along ecological gradients (Braker et al 2001;Angel et al 2010;Liu et al 2014). Many environmental factors were able to shape the archaeal community, such as altitude (Zhang et al 2009), salinity (Jin et al 2011), redox potential (DeAngelis et al 2010, and pH (Tripathi et al 2013). Water regime was observed to be predominant on the archaeal community over regional and seasonal variations, and over the differences between individual habitats in soil (Høj et al 2006).…”