Abstract
Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m2. Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.
Highlights
Nitrification has been the focus of many studies over decades due to the ecological importance of this process, especially for agricultural ecosystems
Numbers of 16S rRNA genes for NS were in the range of 107 to 108 gene copies per g soil dry weight, whereas NB were lower in abundance with 105 to 106 nxrA gene copy numbers
The seasonal dynamics of ammonia-oxidizing archaea (AOA) abundance closely resembled the trend of the NS gene abundance pattern with a decline in August and October and highest values in May and November
Summary
Nitrification has been the focus of many studies over decades due to the ecological importance of this process, especially for agricultural ecosystems. Results of the relative contributions of key players have been contradictory – supportive either of archaeal (Leininger et al, 2006; Adair and Schwartz, 2008; Zhang et al, 2012) or bacterial ammonia-oxidizer (Di et al, 2009; Jia and Conrad, 2009) dominance – or have suffered from missing links between abundances of nitrifiers and nitrification activities (Di et al, 2009) These discrepancies can be explained in part by the designs of those studies, which have focused mainly on detailed analyses of key players involved in one or another sub-process, thereby neglecting to account for the fact that nitrification requires a strong interaction among phylogenetically differing microbes with different ecophysiologies. The last step of the transformation process, the oxidation of nitrite to nitrate, is performed by a distinct group of organisms, the nitrite-oxidizers (Konneke et al, 2005)
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