Unveiling the drivers of ammonia-oxidizer niche partitioning in agricultural soils

Quantifying the coexistence of taxa competing for the same resource is fundamental to community ecology. Organisms which utilize the same resource typically partition their usage of that resource, i.e., their niche, across time, space, and environmental parameters to minimize competition. In the microbial world, the relatively well-studied ammonia-oxidizers compete for ammonia, which they oxidize into nitrite in a process that bottlenecks the global nitrogen cycle. The recent literature calls into question the long-held notion of domain-level niche partitioning for ammonia-oxidizer communities between archaea and bacteria: various examples of within-domain partitioning occurring among closely related taxa calls into question the stereotype of bacteria being copiotrophs while archaea are oligotrophic. Here, we assessed 90 soil and rhizosphere samples from a 36-year long-term field trial and dissected the drivers of ammonia-oxidizer niche partitioning in the agroecosystem. Our methodology consisted of a Illumina MiSeq amplicon sequencing approach targeting archaeal and bacterial amoA sequences, which were then clustered into phylogenetic OTUs. Macroecological niche breadth indices were co-opted to quantify ammonia-oxidizer niche across environmental parameters (Hurlberts niche breadth) and specialization to a given fertilizer regime (Levins niche breadth). Our results suggest that tillage, fertilizer regime, and plant compartment (bulk soil vs rhizosphere) govern ammonia-oxidizer community structure. Furthermore, we show that there are an increased number of archaeal generalists relative to bacterial, and that plant compartment regulates the abundance of generalists. For the first time, we demonstrate that micronutrients regulate the niche partitioning of ammonia-oxidizers both at the domain level and within-domain. We show that while some ammonia-oxidizer clades respond to the various drivers similarly, many closely related phylotypes have different niches. Overall, this study reveals mechanistic insights into the competition between archaeal and bacterial ammonia-oxidizers and provides a framework for investigation of niche partitioning in microbial systems.