Community structure and gene expression analysis for nitrifier enrichment cultures
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摘要: 对采集的长江口潮滩沉积物进行了硝化微生物的富集培养，通过宏基因组技术分析了富集物中硝化微生物的种群结构.检测到4类硝化微生物（占测序总reads的34.7%），包括新近发现的全程氨氧化微生物（complete ammonia oxidizers，comammox）、严格的亚硝酸盐氧化菌Nitrospira、β-变形菌门氨氧化细菌及氨氧化古菌.其中，comammox占硝化微生物类群的48%.此外，基于宏转录组技术分析了4类硝化菌群的基因表达特征（依据Evolutionarygenealogy of genes：Non-supervised Orthologous Groups数据库）.研究探讨了潮滩沉积物富集物中硝化微生物的种群结构与基因表达特征，证明了长江口潮滩沉积环境中comammox的存在，并验证了其基因表达活性.研究结果加深了对河口地区硝化微生物的认识，对于未来硝化过程的分子生态学研究有重要启示意义.Abstract: Nitrifiers were enriched from the tidal sediments of the Yangtze Estuary. Four kinds of nitrifying groups (accounting for 34.7% of the total reads) were detected based on metagenomics, including the recently discovered complete ammonia oxidizers (comammox), strictly nitrite-oxidizing Nitrospira, β-proteobacterial ammonia-oxidizing bacteria, and ammonia-oxidizing archaea. Comammox accounted for 48% of the detected nitrifiers. In addition, gene expression patterns of the nitrifier group (according to the classification in Evolutionary genealogy of genes:Non-supervised Orthologous Groupsdatabase) were analyzed based on metatranscriptomics. The present study showed the community structure and gene expression characteristics of nitrifiers enriched from the tidal sediments, especially the newly discovered comammox. Results enriched our knowledge about the nitrifying communities of estuarine environment, which have great significance to the further molecular ecology research of the nitrification processes.
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Key words:
- nitrifier /
- enrichment culture /
- tidal sediment /
- community structure /
- gene expression
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图 1 培养基及反应器中NH$_{4}^{+}$、NO$_{2}^{-}$、NO$_{3}^{-}$浓度及pH、溶解氧变化趋势
Fig. 1 The variation trend of NH$_{4}^{+}$, NO$_{2}^{-}$, NO$_{3}^{-}$ concentration and pH, dissolved oxygen in medium and enrichment culture
图 2 生物反应器中氨氧化微生物丰度
注: 图中左侧纵坐标表示每ng DNA中AOAamoA的基因拷贝数, 右侧是每ng DNA中$\beta$-AOBamoA的基因拷贝数
Fig. 2 The abundance of ammonia oxidizing microorganisms in the bioreactor system
图 4 生物反应器中硝化菌群丰度
注: 各类群丰度为该类群占硝化菌群的比例.图中内圈表示富集物在种水平上注释到的主要硝化菌群的丰度(右侧图例), 外圈表示富集物中4类硝化菌群的丰度(左侧图例)
Fig. 4 The abundance of nitrifiers in the bioreactor system
图 5 生物反应器中硝化菌群表达量热图
注: 图中NOB指严格亚硝酸盐氧化的NOB, COM指全程氨氧化微生物, AOA指氨氧化古菌, $\beta $-AOB指$\beta $-变形菌门的氨氧化细菌
Fig. 5 Heatmap of gene expression of NOB (strictly nitrite oxidizing Nitrospira), COM (comammox), AOA (ammonia oxidizing archaea), and $\beta $-AOB ($\beta $-proteobacterial ammonia oxidizing)
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