Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China

Abstract

The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.

FIG 1

Map showing the sampling locations of the studied agriculture soils collected from eastern China.

FIG 2

Ratios of AOA to AOB amoA gene copies in the studied soils. The error bars were from three analytical replicates.

FIG 3

UPGMA cluster tree constructed based on the 97% cutoff level-based unweighted Unifrac matrix. Microbial groups with an abundance greater than 2% are displayed. Groups with abundances lower than 2% were included as “Others,” which include Nitrosovibrio and Nitrosomonas clusters 6 and 8. (A) AOB; (B) AOA. For AOB, the previously published nomenclatures of Nitrosospira clusters 0, 1, 2, 3a, 3b, 4, 9, 10, 11, and 12 (7, 8) and Nitrosomonas clusters 5, 6a, 6b, 7, and 8 (9) were used; for AOA, the previously published nomenclatures of Nitrosopumilus, Nitrososphaera, Nitrosocaldus, and Nitrosotalea subclusters and Nitrososphaera sister cluster (23) were used.

FIG 4

Canonical correspondence analysis (CCA) of the AOB and AOA communities (at the OTU level) and measured environmental variables. (A) AOB; (B) AOA.

FIG 5

Variation partition analysis of the effects geographic distance and environmental variables on the phylogenetic structure (at the OTU level) of ammonia-oxidizing microbial populations. “Grp1” contains geographic distance and climatic factors (mean annual temperature and precipitation); “Grp2” denotes soil pH; “Grp3” contains TOC, Micro-C, Micro-C/TOC, Total N, NH₄-N, NO₃-N, and NO₂-N. (A) AOB; (B) AOA.