Community structure of microaerophilic iron-oxidizing bacteria in Japanese paddy field soils
Community structure of microaerophilic iron-oxidizing bacteria in Japanese paddy field soils
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DOI：
10.1080/00380768.2019.1671139
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发表时间：
2019-09
影响因子：
2
通讯作者：
Tatsushi Naruse;Y. Ban;Tomofumi Yoshida;Takahiro Kato;Mari Namikawa;Tomoki Takahashi;M. Nishida;S. Asakawa;Takeshi Watanabe
中科院分区：
文献类型：
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作者：
Tatsushi Naruse;Y. Ban;Tomofumi Yoshida;Takahiro Kato;Mari Namikawa;Tomoki Takahashi;M. Nishida;S. Asakawa;Takeshi Watanabe
摘要 铁（Fe）的氧化还原循环是稻田土壤生物地球化学的核心过程。尽管 Fe(II) 氧化过程是由非生物和生物反应介导的，但参与该过程的微生物在稻田土壤中尚未得到充分研究。本研究调查了日本中部（安城）和东北部（大曲）稻田犁层中的微需氧 Fe(II) 氧化细菌 (FeOB) 的群落结构，因为该科成员是环中性淡水环境中的典型 FeOB，可能对稻田土壤中的 Fe(II) 氧化具有重要作用。新设计了针对 Gallionella 相关 FeOB 16S rRNA 基因的引物组，用于聚合酶链式反应-变性梯度凝胶电泳 (PCR-DGGE) 和定量 PCR (qPCR) 分析。 DGGE 分析显示现场站点之间的带模式存在显着差异。此外，在每年的水稻种植实践中，安城市田地的土壤深度（0-1厘米和1厘米以下）之间的模式存在微小差异，而大曲田的模式相对稳定。总共对 54 个条带进行了测序，并根据 97% 的相似度聚类成 20 个操作分类单元 (OTU)。 20 个 OTU 中的 18 个（54 个带中的 50 个）属于 Gallionellaceae 的 FeOB 簇，其中一些与已知的微需氧 FeOB、Ferrigenium kumadai、Ferriphaselus amnicola、‘Sideroxydans lithotropicus’和‘S.帕卢迪科拉’。两块稻田中16S rRNA基因拷贝数分别为105~107和106~108拷贝g−1干土，与水稻种植期间土壤中乙酸可提取Fe(II)含量呈负相关。这些结果表明存在相当数量的多种与 Gallionella 相关的 FeOB 及其潜在参与土壤的 Fe(II) 氧化过程，特别是在稻田土壤的水稻种植期间。
ABSTRACT Redox cycle of iron (Fe) is the central process in the biogeochemistry of paddy field soil. Although Fe(II)-oxidizing process is mediated by both abiotic and biotic reactions, microorganisms involved in the process have not been well studied in paddy field soil. The present study investigated the community structure of microaerophilic Fe(II)-oxidizing bacteria (FeOB) in the family Gallionellaceae in the plow layer of paddy fields located in the central (Anjo) and northeastern (Omagari) Japan since the members in the family are the typical FeOB in circumneutral freshwater environments and possibly have the significant role for Fe(II) oxidation in paddy field soils. A primer set targeting 16S rRNA gene of Gallionella-related FeOB was newly designed for the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR (qPCR) analyses. DGGE analysis showed significant differences in the band patterns between the field sites. Besides, minor differences were observed in the patterns between the soil depths (0–1 cm and below 1 cm) in the Anjo field, while the patterns were relatively stable in the Omagari field during the annual rice cultivation practices. In total 54 bands were sequenced and clustered into 20 operational taxonomic units (OTUs) on the basis of the 97% similarity. Eighteen out of twenty OTUs (50 of 54 bands) were affiliated within the FeOB cluster of Gallionellaceae, some of which were clustered with known microaerophilic FeOB, Ferrigenium kumadai, Ferriphaselus amnicola, ‘Sideroxydans lithotrophicus’ and ‘S. paludicola’. The number of the 16S rRNA gene copies was 105–107 and 106–108 copies g−1 dried soil in the two paddy fields and negatively correlated to the contents of acetate-extractable Fe(II) in the soils during the rice cultivation period. These results suggested inhabitance of considerable number of diverse Gallionella-related FeOB and their potential involvement in the Fe(II)-oxidizing process of soil, especially during the rice cultivation period in the paddy field soils.