Partitioning Nitrospira community structure and co-occurrence patterns in a long-term inorganic and organic fertilization soil

Abstract

Unraveling the drivers of the nitrogen cycling functional guilds variation in response to fertilizer management is a major goal in agroecosystem study. Nitrospira-like nitrite oxidizing bacteria can oxidize nitrite to nitrate, which play a critical role in the biogeochemical nitrogen cycle. However, how the Nitrospira community structure and co-occurrence patterns in a long-term inorganic and organic fertilization regimes within different soil aggregates have been largely unexplored. The soil samples were collected from a long-term (39-year) inorganic and organic fertilized agricultural ecosystem, including no-fertilizer (CK); mineral-fertilizer (NPK); manure-fertilizer (M); nitrogen-fertilizer (N); and M + N (MN). Three sizes of soil aggregate were manually fractionated by soil wet sieving technique with a series of meshes: (i) 2000–250 μm (macroaggregates), (ii) 250–53 μm (microaggregates), and (iii) < 53 μm fractions (silt and clay). We performed qPCR and high-throughput-sequencing to assess the Nitrospira abundance and community structure, respectively. Organic fertilization (M and MN) efficiently increased soil potential nitrite oxidation activity (PNO), which was higher in the < 53 μm than 250–53 μm and followed the 2000–250 μm fraction, than other treatments. All the fertilizer treatments resulted in a similar pattern, where the 250–53-μm fraction had significantly greater Nitrospira abundance than the 2000–250 μm and < 53 μm fractions. The alpha diversity of Nitrosipra did not change in response to the fertilization treatments and soil aggregate sizes. Nitrospira community shifted in fertilization types, while not in aggregate sizes. Nitrospira community composition and abundance significantly correlated with PNO. Network analysis suggested that organic fertilizations (M and MN) promote the complexity of Nitrospira networks and possess higher connectivity than inorganic fertilization networks. Our data suggested that fertilization strongly affected the Nitrospira community structure and co-occurrence patterns, which may implicate the importance of Nitrospira function in the nitrite oxidation process in soils with organic fertilization.