Gruber-Dorninger Christiane, Pester Michael, Kitzinger Katharina, Savio Domenico F, Loy Alexander, Rattei Thomas, Wagner Michael, Daims Holger
Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
ISME J. 2015 Mar;9(3):643-55. doi: 10.1038/ismej.2014.156. Epub 2014 Aug 22.
Nitrospira are chemolithoautotrophic nitrite-oxidizing bacteria that catalyze the second step of nitrification in most oxic habitats and are important for excess nitrogen removal from sewage in wastewater treatment plants (WWTPs). To date, little is known about their diversity and ecological niche partitioning within complex communities. In this study, the fine-scale community structure and function of Nitrospira was analyzed in two full-scale WWTPs as model ecosystems. In Nitrospira-specific 16S rRNA clone libraries retrieved from each plant, closely related phylogenetic clusters (16S rRNA identities between clusters ranged from 95.8% to 99.6%) within Nitrospira lineages I and II were found. Newly designed probes for fluorescence in situ hybridization (FISH) allowed the specific detection of several of these clusters, whose coexistence in the WWTPs was shown for prolonged periods of several years. In situ ecophysiological analyses based on FISH, relative abundance and spatial arrangement quantification, as well as microautoradiography revealed functional differences of these Nitrospira clusters regarding the preferred nitrite concentration, the utilization of formate as substrate and the spatial coaggregation with ammonia-oxidizing bacteria as symbiotic partners. Amplicon pyrosequencing of the nxrB gene, which encodes subunit beta of nitrite oxidoreductase of Nitrospira, revealed in one of the WWTPs as many as 121 species-level nxrB operational taxonomic units with highly uneven relative abundances in the amplicon library. These results show a previously unrecognized high diversity of Nitrospira in engineered systems, which is at least partially linked to niche differentiation and may have important implications for process stability.
硝化螺旋菌是化能无机自养型亚硝酸盐氧化细菌，在大多数有氧环境中催化硝化作用的第二步，对污水处理厂（WWTPs）从污水中去除过量氮至关重要。迄今为止，对于它们在复杂群落中的多样性和生态位划分了解甚少。在本研究中，以两个全规模污水处理厂作为模型生态系统，分析了硝化螺旋菌的精细群落结构和功能。在从每个工厂获取的硝化螺旋菌特异性16S rRNA克隆文库中，发现了硝化螺旋菌谱系I和II内密切相关的系统发育簇（簇间16S rRNA同一性范围为95.8%至99.6%）。新设计的荧光原位杂交（FISH）探针能够特异性检测其中几个簇，并显示它们在污水处理厂中持续共存了数年。基于FISH的原位生态生理学分析、相对丰度和空间排列定量以及微放射自显影揭示了这些硝化螺旋菌簇在偏好的亚硝酸盐浓度、利用甲酸盐作为底物以及与氨氧化细菌作为共生伙伴的空间共聚集方面的功能差异。对编码硝化螺旋菌亚硝酸盐氧化还原酶β亚基的nxrB基因进行扩增子焦磷酸测序，在其中一个污水处理厂的扩增子文库中发现多达121个物种水平的nxrB操作分类单元，其相对丰度极不均衡。这些结果表明，工程系统中硝化螺旋菌具有此前未被认识到的高度多样性，这至少部分与生态位分化有关，可能对工艺稳定性具有重要意义。
