Role of generalists, specialists and opportunists in Nitrospira community assembly in soil aggregates from nearby cropland and grassland areas in a campus

Abstract

Nitrospirota is an essential contributor to nitrification. However, the community assembly mechanism of such organisms in soil aggregates from nearby but different ecosystems is unclear. We quantitatively measured the relative contributions of generalists, opportunists and specialists to the Nitrospira community assembly. Nitrospira were more abundant in agricultural soils than in grasslands and were relatively enriched in microaggregates in both agricultural (AS) and grassland soils (GS). These findings could be explained by the neutral pH of AS and the relatively high organic carbon quantity of the aggregates. The community variation in Nitrospira was driven by both ecosystem and aggregate size fractions, with dispersal and drift dominating the assembly process, partly explained by macro- and microaggregates with higher organic quality that can reduce selection pressures to enrich Nitrospira species (indicated by a higher α diversity), supporting more stochastic processes (drift and dispersal limitations) in community assembly. Generalists belonging to Namibia soil cluster 2, followed by unknown Nitrospira and other lineage II members, contributed to the stochastic assembly, as indicated by a high normalized stochasticity ratio (NST) value of 0.618. A total of 89.7 % and 5.6 % of the ASVs were defined as opportunists and generalists, respectively. Opportunists expand their taxonomic affiliation from Nitrospira lineages I, II, V, and grassland metagenome lineages to unknown lineages, and almost all specialists cannot be assigned to a known lineage or a subcluster. We observed that the NSTs for Opportunists and specialists were approximately 0.472 and 0.247, respectively, suggesting that the assembly of opportunists was less dominated by stochastic processes than was that of generalists, while the assembly of specialists highly relied on deterministic processes. Indeed, limited variation in the abundances of opportunists and specialists was significantly explained by the soil properties, agreeing that variable selection slightly contributed to Nitrospira community assembly. We also highlighted that each specialist with an unknown affiliation could be a new species or variant from Nitrospira in “specific” micro-environments, as indicated by the fact that one species occurred in only a few soil aggregate size fractions. The present study presents a case in which the stochastic process of Nitrospira community assembly in soil aggregates from two nearby ecosystems with mild environmental conditions could be explained by a high proportion of opportunists plus generalists and a few microhabitat specialists.