North Dakota State University Fargo, North Dakota, United States
Abstract: Ammonia-oxidizing microbes are vital to the global nitrogen cycle. The ecology of these microbes is particularly important in agroecosystems as ammonia oxidation can modulate nitrogen availability for plants, as well as the production of the greenhouse gas nitrous oxide and the leaching of nitrogen into waterways. Traditionally, the literature held that archaeal ammonia oxidizers tend to be oligotrophic in the sense of them being better adapted to low ammonium, low pH environments, while the usually copiotrophic bacteria tend to be better adapted to higher ammonium and higher pH environments. However, the recent literature on soil ammonia-oxidizing microbes calls into question the idea of this Domain-level niche partitioning, with various counterexamples arising through culturing. It remains unclear what role fertilizer regime, and subsequently soil abiotic factors, play in the niche partitioning of ammonia-oxidizing microbes in agroecosystems. In this study, we aim to elucidate these ecological drivers of niche differentiation in ammonia-oxidizing microbes through a phylogenetic, network-based approach. We hypothesized that closely related phylogenetic groups should respond similarly to abiotic stimuli. Our approach utilized Illumina MiSeq amplicon sequencing to target the amoA gene of archaeal and bacterial ammonia oxidizers in soil collected from a 35-year crop rotation field trial comprising of various types of fertilizer amendments. We found that the community structure of both archaea and bacteria significantly changes across fertilizer regime. Interestingly, we found a large increase in archaeal phylotype richness in the organic fertilizer treatment relative to the bacteria, indicating Domain niche differentiation under organic conditions but not in the other fertilizer treatments. Co-occurrence networks revealed that a Nitrosospira phylotype is a keystone taxon in the system, governing the associations of other phylotypes. Levin’s niche breadth indicated that archaea tend to be generalists while bacteria are specialists and are much more affected by fertilizer regime. We further interrogated this niche differentiation by assessing Hurlbert’s niche breadth, revealing the tendency for a small subset of bacterial specialists adapted to a given nitrogen, pH, or micronutrient level, while the archaea tend to be generalists and are less affected by nitrogen, pH, and micronutrient levels. Our results suggest that niche differentiation seems to be stronger within Domain than between Domain, with similar phylogenetic groups filling similar niches as predicted. Overall, this study reveals mechanistic insights into the competition between archaea and bacteria ammonia oxidizers and how their niches are partitioned across fertilizer regime and soil abiotic factors.
