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Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

Tago K, Okubo T, Shimomura Y, Kikuchi Y, Hori T, Nagayama A, Hayatsu M - Microbes Environ. (2014)

Bottom Line: The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields.The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test.These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

View Article: PubMed Central - PubMed

Affiliation: Environmental Biofunction Division, National Institute for Agro-Environmental Sciences.

ABSTRACT
The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Show MeSH
Abundances of AOB and AOA amoA genes in soil samples.
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f1-30_21: Abundances of AOB and AOA amoA genes in soil samples.

Mentions: The abundances of the AOB and AOA amoA genes, which reflected the AOB and AOA populations, were determined by qPCR (Fig. 1). The abundances of AOB amoA genes were estimated to be in the range of 1.8 × 105 to 9.2 × 106 gene copies g dry soil−1. The E7 soil sample that received poultry manure combined with urea fertilization (Table S1) had the highest abundance of the AOB amoA gene. The abundances of the AOA amoA genes were estimated to be in the range of 1.7 × 106 to 5.3 × 107 gene copies g dry soil−1. The E7 field also had the highest abundance of the AOA amoA gene among all the soil samples tested. The abundance of AOB amoA was higher than that of AOA in only the A2 soil sample. The ratios of the AOA amoA gene to the AOB amoA gene ranged from 0.87 to 22.70 among all the soil samples tested.


Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

Tago K, Okubo T, Shimomura Y, Kikuchi Y, Hori T, Nagayama A, Hayatsu M - Microbes Environ. (2014)

Abundances of AOB and AOA amoA genes in soil samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356460&req=5

f1-30_21: Abundances of AOB and AOA amoA genes in soil samples.
Mentions: The abundances of the AOB and AOA amoA genes, which reflected the AOB and AOA populations, were determined by qPCR (Fig. 1). The abundances of AOB amoA genes were estimated to be in the range of 1.8 × 105 to 9.2 × 106 gene copies g dry soil−1. The E7 soil sample that received poultry manure combined with urea fertilization (Table S1) had the highest abundance of the AOB amoA gene. The abundances of the AOA amoA genes were estimated to be in the range of 1.7 × 106 to 5.3 × 107 gene copies g dry soil−1. The E7 field also had the highest abundance of the AOA amoA gene among all the soil samples tested. The abundance of AOB amoA was higher than that of AOA in only the A2 soil sample. The ratios of the AOA amoA gene to the AOB amoA gene ranged from 0.87 to 22.70 among all the soil samples tested.

Bottom Line: The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields.The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test.These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

View Article: PubMed Central - PubMed

Affiliation: Environmental Biofunction Division, National Institute for Agro-Environmental Sciences.

ABSTRACT
The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Show MeSH