Nitrifier community assembly and species co-existence in forest and meadow soils across four sites in a temperate to tropical region

Abstract

Nitrification is a central process in terrestrial N cycling. However, the role of diversity of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in shaping nitrifier communities remains underexplored. This study deciphered the nitrifier community assembly by analyzing amplicon sequence variants (ASVs) of amoA and nxrB genes from soil microbiomes in forest and meadow ranging from the temperate monsoon to the tropic monsoon climate areas. The abundance, α-diversity, and β-diversity of AOA, AOB, Nitrobacter, and Nitrospira were dominantly distinguished by geographical variation and less by vegetation type. The overall environmental factors, including the soil properties and climate factors, significantly correlated with the β-diversity of AOA and Nitrospira, but not with AOB and Nitrobacter community. The assembly process of AOA was dominated by heterogeneous selection, while that of AOB, Nitrobacter, and Nitrospira by dispersal limitation. We found that AOA and Nitrospira dominated the combined nitrifier network, and several phylotypes exhibited extensive segregation between different modules, suggesting niche partition was present within subgroups or lineages of AOA, AOB, and Nitrospira. Links between different functional groups might reflect functional coupling, while links between the same lineage or subgroup could result from niche overlap or unknown mechanisms. As network connectors, some AOA and Nitrospira belonged to generalists, which could be essential to keep the stability of the network. Nitrospira inopinata-like node in module 24 suggested that comammox might not be an ecologically isolated bacterium in nitrification. We hypothesized that a balance between species sorting in AOA and dispersal limitation in AOB and NOB communities determined the species co-existence in the forest and meadow soils from temperate to tropical regions. This study might enhance our understanding of contemporary co-existence in different functional groups driving nitrification.