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Bacterial community structures of a Fe-Mn nodule sample and its surrounding soil were investigated using PCR, amplified ribosomal DNA restriction analysis, cloning and sequencing methods. Result showed that phylogenetically diverse bacteria were present in the nodule and soil samples, and Acidobacteria- and Proteobacteria-affiliated bacteria dominated in both samples. However, Firmicutes were only found in the nodules, while the soil had much more Acidobacteria and Verrucomicrobia than the nodules. Many clones retrieved in this study closely resembled the clones previously obtained from environments with high metal contents. These findings may shed light on the biological formation of Mn oxides in soil environment. [ABSTRACT FROM AUTHOR]

The discovery of comammox Nitrospira has expanded our knowledge of classical labor division in nitrification and opened up new avenues to unravel the nitrification process in terrestrial ecosystems. However, the effects of fertilization and rhizosphere on comammox Nitrospira remains largely limited, especially in alkaline agricultural soils. To address this knowledge gap, the community structure of comammox Nitrospira and canonical ammonia oxidizers in the bulk and rhizosphere of an alkaline agricultural soil following 8 years of fertilizer applications was investigated. The fertilization treatments included no fertilization (CON), mineral NPK fertilizer (NPK), manure + straw (MS), NPK + manure (NPKM), NPK + manure and straw (NPKMS), and NPK + manure and straw by deep ploughing (NPKMSD). Five phylogenetic clusters of comammox Nitrospira were detected in the soil including clades A.1, A.2.1, A.2.2, A.3 and B, with A.2.1 and B as the dominant clades. Fertilization had a greater effect than rhizosphere on the community structure of comammox Nitrospira , while both fertilization and rhizosphere had no significant effect on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Compared with CON and NPK, the relative abundance of comammox Nitrospira clade A, especially clade A.2.1, increased while clade B decreased following manure applications. Soil nitrate played a critical role in driving the variation of comammox Nitrospira community structure. These findings showed novel evidence of niche specialization of comammox Nitrospira and canonical ammonia oxidizers in agricultural soils. • Fertilization impacted more on comammox Nitrospira than canonical ammonia oxidizers. • Comammox Nitrospira clade B dominated in the alkaline agricultural soils. • Clade A.2.1 increased, but clade B decreased with manure application. • Nitrate might be an important driver shaping comammox Nitrospira community structure. [ABSTRACT FROM AUTHOR]