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Stable Isotope Probing Analysis of Interactions between Ammonia Oxidizers

机译：氨氧化器之间相互作用的稳定同位素探测分析

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The response of natural microbial communities to environmental change can be assessed by determining DNA- or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a ~(13)C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with ~(13)C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA- and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.
机译：天然微生物群落对环境变化的反应可以通过使用指纹技术（例如变性梯度凝胶电泳）（分别为DNA-DGGE和RNA-DGGE）确定16S rRNA基因序列相对丰度的DNA或RNA靶向变化来评估。或与〜（13）C标记的底物（DNA-SIP-DGGE）孵育后，通过16S rRNA基因的稳定同位素探测（SIP）。在包含两个或三个对高氨氮浓度具有不同耐受性的纯净或富集硝化螺菌培养物的社区的分批生长过程中，比较了这三种方法的敏感性。向培养物提供低，中或高初始氨浓度以及〜（13）C标记的二氧化碳。 DNA-SIP-DGGE为生长提供了最直接的证据，并且是最敏感的，在DNA-和RNA-DGGE谱发生变化之前以及在亚硝酸盐和硝酸盐产量可检测到的增加之前，DGGE谱发生了明显变化。 RNA-DGGE具有中等敏感性。另外，这三种分子方法被用来追踪社区内单个菌株的生长。通常，可以从单一养殖的生长特征预测社区内单个菌株相对活动的变化。在所有氨气浓度下，耐氨性亚硝基螺菌簇3b菌株在混合群落中均占优势，而在中等氨气浓度下，氨敏感菌在竞争中胜于竞争。但是，在最低氨浓度下会出现耐氨和氨敏感菌株的共存，在某些条件下，单培养中高氨抑制的菌株在混合培养中在高氨下具有活性，并与耐氨菌株共存。因此，结果证明了SIP对检测相对较低产量和较低活性的生物活性的敏感性，以及其跟踪相互作用的微生物群落结构变化的能力。

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