Abundance and composition of ammonia‐oxidizing bacteria and ammonia‐oxidizing archaea communities of an alkaline sandy loam

Abstract

SummaryThe abundance and composition of soil ammoniaoxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities under different long-term (17 years) fertilization practices were investigated using real-time polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE) The highest bacterial amoA gene copy numbers were found in those treatments receiving N fertilizer. The archaeal amoA gene copy numbers ranging from 1.54 ¥ 10 7 to 4.25 ¥ 10 7 per gram of dry soil were significantly higher than those of bacterial amoA genes, ranging from 1.24 ¥ 10 5 to 2.79 ¥ 10 6 per gram of dry soil, which indicated a potential role of AOA in nitrification. Ammonia-oxidizing bacteria abundance had significant correlations with soil pH and potential nitrification rates. Denaturing gradient gel electrophoresis patterns revealed that the fertilization resulted in an obvious change of the AOB community, while no significant change of the AOA community was observed among different treatments. Phylogenetic analysis showed a dominance of Nitrosospiralike sequences, while three bands were affiliated with the Nitrosomonas genus. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). These results suggest that longterm fertilization had a significant impact on AOB abundance and composition, while minimal on AOA in the alkaline soil..

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition

“…Phylogenetic analysis was conducted using MEGA version 5.0. Diversity indices such as Shannon index (H) and Evenness index (E) were measured as described in our earlier articles (Shen et al 2008;Subrahmanyam et al 2014c). The range-weighted richness Rr index was determined to understand the broader carrying capacity of the soils for microbial groups (Subrahmanyam et al 2014c).…”

Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India

“…The total volume of PCR mixture was 50 μl including 10× Ex Taq™ buffer, 3.0 mM MgCl 2 , 250 μM each of dNTP, 2.5 U Ex Taq™ DNA polymerase (TaKaRa Bio), primers (0.2 μM each primer), and BSA (1 μg ml −1 ). Detailed thermal profiles of the primers have been described in previous studies (Ge et al 2008;Shen et al 2008). PCR products of bacterial and archaeal amoA genes were loaded onto 8 %w/v polyacrylamide gels (acrylamidebisacrylamide [37.5:1]) with a denaturing gradient of 40-60 and 15-55 % (100 % denaturing solution contains 7 M urea and 40 % formamide), respectively.…”

“…Translated amino acid sequences (for both AOA-amoA and AOB-amoA genes) were used to construct neighbor-joining tree followed by Poisson model with 1,000 replicates to produce bootstrap values. Diversity indices such as Shannon index (H) and Evenness index (E) were measured as described in our earlier articles (Shen et al 2008;Zhou et al 2011).…”

The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

“…We do know that distinct soils often harbor distinct AOB communities. A number of environmental factors, including vegetation type [9][10][11], soil nutrient levels [12][13][14][15][16], soil microclimate [13,17,18], and management practices [19][20][21], have been found to have an important influence on the spatial variability exhibited by AOB communities. However, because most studies have compared AOB communities across a rather limited number of samples, with one notable exception being the study by Avrahami and Conrad [18], it has been difficult to ascertain which soil biotic and abiotic characteristics are related to AOB community composition across larger spatial scales.…”