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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.

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Relative abundance of AOB amoA OTUs (A) and the UPGMA cluster tree (B). The relative abundances in panel A show the average of three replicates. The OTU numbers are followed by the Nitrosospira cluster numbers, which are given in parentheses. The cluster tree in panel B was constructed using the average of three replicates.
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f2-30_21: Relative abundance of AOB amoA OTUs (A) and the UPGMA cluster tree (B). The relative abundances in panel A show the average of three replicates. The OTU numbers are followed by the Nitrosospira cluster numbers, which are given in parentheses. The cluster tree in panel B was constructed using the average of three replicates.

Mentions: The community structures of AOB were characterized by a 454-pyrosequencing analysis of the AOB amoA genes. A total of 61,096 AOB amoA gene sequence reads were obtained in triplicate from eight soil samples after excluding chimeric and low-quality sequences (Table S2). The average number of sequence reads in each field was 7,637, and ranged from 5,375 to 11,158. These high quality sequence reads, except for low-abundance OTU (< 0.5% in all samples) sequences, were clustered into 15 OTUs at the 5% cut-off. The representative sequences from dominant OTUs were used in the phylogenetic analysis. We used cluster identification for the AOB amoA genes, which was defined previously by Avrahami and Conrad (1). The phylogenetic analysis indicated that all AOB amoA OTUs found in the farmed soils were affiliated exclusively with the Nitrosospira genus and were placed into clusters 3a, 3b, and 9 (Fig. S2). OTU2 and OTU10 were grouped in cluster 9 and 3b, respectively and the remaining 13 OTUs were grouped in cluster 3a. The average relative OTU abundances from triplicate readings are shown in Fig. 2A and Table S3. Cluster 3a was the most dominant among all soil samples, and cluster 9 (OTU2) was one of the major components in samples D1, D2, and E2, but was minor or undetectable in the other samples. Cluster 3a was a major component in all groups, but its OTU composition differed among the groups. For example, OTU1 was the most abundant and occupied over 50% in A1, A2, B7, D1, and E2 soil samples. However, OTU1 was less abundant in C1 and D2 soil samples and was not detected in the E7 soil sample.


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)

Relative abundance of AOB amoA OTUs (A) and the UPGMA cluster tree (B). The relative abundances in panel A show the average of three replicates. The OTU numbers are followed by the Nitrosospira cluster numbers, which are given in parentheses. The cluster tree in panel B was constructed using the average of three replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2-30_21: Relative abundance of AOB amoA OTUs (A) and the UPGMA cluster tree (B). The relative abundances in panel A show the average of three replicates. The OTU numbers are followed by the Nitrosospira cluster numbers, which are given in parentheses. The cluster tree in panel B was constructed using the average of three replicates.
Mentions: The community structures of AOB were characterized by a 454-pyrosequencing analysis of the AOB amoA genes. A total of 61,096 AOB amoA gene sequence reads were obtained in triplicate from eight soil samples after excluding chimeric and low-quality sequences (Table S2). The average number of sequence reads in each field was 7,637, and ranged from 5,375 to 11,158. These high quality sequence reads, except for low-abundance OTU (< 0.5% in all samples) sequences, were clustered into 15 OTUs at the 5% cut-off. The representative sequences from dominant OTUs were used in the phylogenetic analysis. We used cluster identification for the AOB amoA genes, which was defined previously by Avrahami and Conrad (1). The phylogenetic analysis indicated that all AOB amoA OTUs found in the farmed soils were affiliated exclusively with the Nitrosospira genus and were placed into clusters 3a, 3b, and 9 (Fig. S2). OTU2 and OTU10 were grouped in cluster 9 and 3b, respectively and the remaining 13 OTUs were grouped in cluster 3a. The average relative OTU abundances from triplicate readings are shown in Fig. 2A and Table S3. Cluster 3a was the most dominant among all soil samples, and cluster 9 (OTU2) was one of the major components in samples D1, D2, and E2, but was minor or undetectable in the other samples. Cluster 3a was a major component in all groups, but its OTU composition differed among the groups. For example, OTU1 was the most abundant and occupied over 50% in A1, A2, B7, D1, and E2 soil samples. However, OTU1 was less abundant in C1 and D2 soil samples and was not detected in the E7 soil sample.

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