The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria
The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria
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DOI：
10.1111/j.1462-2920.2008.01701.x
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发表时间：
2008-11-01
影响因子：
5.1
通讯作者：
Prosser, James I.
中科院分区：
文献类型：
--
作者：
Nicol, Graeme W.;Leininger, Sven;Prosser, James I.
自养氨氧化发生在酸性土壤中，即使分离的氨氧化细菌的实验室培养物不能在中性ph以下生长。为了研究具有氨单加氧酶基因的古细菌是否负责酸性土壤中的自养硝化，采用16S rRNA和amoA基因扩增、变性梯度凝胶电泳（DGGE）和序列分析等方法，测定了不同pH（4.9 ~ 7.5）梯度下氨氧化菌和古细菌的群落结构和系统发育。两种群落的结构随土壤pH值的变化而变化，在酸性和中性土壤中种群分布明显。对crenarchaeal 16S rRNA和amoA基因的系统发育重建证实了在pH梯度内不同谱系的选择，系统发育的高度相似性表明16S rRNA和amoA基因高度一致。在不同的pH梯度下，古细菌和细菌的amoA基因拷贝数和mRNA转录物的丰度进行了对比。古细菌的amoA基因和转录本丰度随着土壤pH值的增加而降低，而细菌的amoA基因丰度普遍降低，转录本丰度随着pH值的增加而增加。在酸性或中性土壤或pH值调整为原生土壤的混合土壤中，通过DGGE分析基因转录本的短期活性。虽然混合土壤微生物中含有相同的古细菌氨氧化剂群落，但那些适应酸性或中性pH范围的微生物在其原生土壤pH下表现出更大的相对活性。研究结果表明，不同pH的土壤中选择了不同的细菌和古细菌氨氧化剂种型，这些群落结构和丰度的差异反映在对氨氧化剂活性的不同贡献上。他们还表明，这两组氨氧化剂具有不同的生理特性和生态位，对酸性土壤的硝化作用有影响。
Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.