Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia

Abstract

Nitrification, the oxidation of NH 4 þ to NO 2 À and subsequently to NO 3 À , plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammoniaoxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.

Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary

“…b-AOB genes, in contrast, were only detected in 59% of samples and in much lower abundance. This result is consistent with an earlier study of subtropical estuarine sediment, which showed that AOA are ubiquitous in sediments, whereas b-AOB were found in only 40% of samples (Beman and Francis, 2006) and suggests that AOA and not AOB may be responsible for the majority of nitrification in estuarine sediments (Caffrey et al, 2007;Lam et al, 2007). The lack of consistent correlation in the abundance of AOA and b-AOB, suggests that there are different factors driving their proliferation in the Fitzroy river.…”

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

“…Decreasing soil temperature was correlated with increasing AOA abundance, which is in contrast to the results of a soil microcosm study by Tourna et al (2008). However, Urakawa et al (2008) and Caffrey et al (2007) investigated marine ecosystems in which decreased phylogenetic diversity and abundance of AOA were found with increasing temperature, respectively. Based on these contradictory results, we suggest further experiments under field conditions to substantiate that decreasing soil temperature promotes AOA abundance.…”

Significance of archaeal nitrification in hypoxic waters of the Baltic Sea

“…These studies often revealed the dominance of archaeal over bacterial ammonia oxidizers (Francis et al, 2005;Wuchter et al, 2006;Mincer et al, 2007;Agogué et al, 2008;Newell et al, 2013). Further support for the strong role for AOA in nitrification comes from observations of the co-occurrence of archaeal amoA in areas of nitrification activity (Caffrey et al, 2007;Beman et al, 2008;Alves et al, 2013) and from metatranscriptomic studies (Baker et al, 2012;Lesniewski et al, 2012). However, to determine the actual contribution and impact of AOA on the nitrogen cycle requires measurements of ammonium oxidation rates, as they cannot be deduced from transcript abundance alone (Mu mann et al, 2011), given that quantification is influenced by, for example, mRNA degradation during sampling (Feike et al, 2012) and, in addition, may not inevitably reflect environmental activity.…”