Ishii Satoshi, Joikai Kazuki, Otsuka Shigeto, Senoo Keishi, Okabe Satoshi
Department of Soil, Water, and Climate; BioTechnology Institute, University of Minnesota.
Microbes Environ. 2016 Sep 29;31(3):293-8. doi: 10.1264/jsme2.ME16001. Epub 2016 Jul 15.
Pseudogulbenkiania is a relatively recently characterized genus within the order Neisseriales, class Betaproteobacteria. This genus contains several strains that are capable of anaerobic, nitrate-dependent Fe(II) oxidation (NDFO), a geochemically important reaction for nitrogen and iron cycles. In the present study, we examined denitrification functional gene diversities within this genus, and clarified whether other Pseudogulbenkiania sp. strains perform denitrification and NDFO. Seventy strains were analyzed, including two type strains, a well-characterized NDFO strain, and 67 denitrifying strains isolated from various rice paddy fields and rice-soybean rotation fields in Japan. We also attempted to identify the genes responsible for NDFO by mutagenesis. Our comprehensive analysis showed that all Pseudogulbenkiania strains tested performed denitrification and NDFO; however, we were unable to obtain NDFO-deficient denitrifying mutants in our mutagenesis experiment. This result suggests that Fe(II) oxidation in these strains is not enzymatic, but is caused by reactive N-species that are formed during nitrate reduction. Based on the results of the comparative genome analysis among Pseudogulbenkiania sp. strains, we identified low sequence similarity within the nos gene as well as different gene arrangements within the nos gene cluster, suggesting that nos genes were horizontally transferred. Since Pseudogulbenkiania sp. strains have been isolated from various locations around the world, their denitrification and NDFO abilities may contribute significantly to nitrogen and iron biogeochemical cycles.
假古尔本基尼亚属是β-变形菌纲奈瑟菌目中一个相对较新被鉴定的属。该属包含多个能够进行厌氧、硝酸盐依赖的亚铁氧化（NDFO）的菌株，这是氮和铁循环中一个对地球化学具有重要意义的反应。在本研究中，我们检测了该属内的反硝化功能基因多样性，并阐明了其他假古尔本基尼亚属菌株是否进行反硝化和NDFO。我们分析了70个菌株，包括两个模式菌株、一个特征明确的NDFO菌株以及从日本各种稻田和稻豆轮作田中分离出的67个反硝化菌株。我们还试图通过诱变鉴定负责NDFO的基因。我们的综合分析表明，所有测试的假古尔本基尼亚属菌株都进行反硝化和NDFO；然而，在我们的诱变实验中未能获得缺乏NDFO的反硝化突变体。这一结果表明，这些菌株中的亚铁氧化不是由酶催化的，而是由硝酸盐还原过程中形成的活性氮物种引起的。基于假古尔本基尼亚属菌株间比较基因组分析的结果，我们在nos基因中发现了低序列相似性以及nos基因簇内不同的基因排列，这表明nos基因是水平转移的。由于假古尔本基尼亚属菌株已从世界各地不同地点分离得到，它们的反硝化和NDFO能力可能对氮和铁的生物地球化学循环有显著贡献。
