Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.
ISME J. 2011 May;5(5):866-78. doi: 10.1038/ismej.2010.172. Epub 2010 Nov 18.
Quantitative PCR (qPCR) analysis revealed elevated relative abundance (1.8% of prokaryotes) of marine group 1 Crenarchaeota (MG1C) in two samples of southeastern US coastal bacterioplankton, collected in August 2008, compared with samples collected from the same site at different times (mean 0.026%). We analyzed the MG1C sequences in metatranscriptomes from these samples to gain an insight into the metabolism of MG1C population growing in the environment, and for comparison with ammonia-oxidizing bacteria (AOB) in the same samples. Assemblies revealed low diversity within sequences assigned to most individual MG1C open reading frames (ORFs) and high homology with 'Candidatus Nitrosopumilus maritimus' strain SCM1 genome sequences. Reads assigned to ORFs for ammonia uptake and oxidation accounted for 37% of all MG1C transcripts. We did not recover any reads for Nmar_1354-Nmar_1357, proposed to encode components of an alternative, nitroxyl-based ammonia oxidation pathway; however, reads from Nmar_1259 and Nmar_1667, annotated as encoding a multicopper oxidase with homology to nirK, were abundant. Reads assigned to two homologous ORFs (Nmar_1201 and Nmar_1547), annotated as hypothetical proteins were also abundant, suggesting that their unknown function is important to MG1C. Superoxide dismutase and peroxiredoxin-like transcripts were more abundant in the MG1C transcript pool than in the complete metatranscriptome, suggesting an enhanced response to oxidative stress by the MG1C population. qPCR indicated low AOB abundance (0.0010% of prokaryotes), and we found no transcripts related to ammonia oxidation and only one RuBisCO transcript among the transcripts assigned to AOB, suggesting they were not responding to the same environmental cues as the MG1C population.
定量 PCR（qPCR）分析显示，与在不同时间从同一地点采集的样本相比（平均值为 0.026%），2008 年 8 月采集的美国东南部沿海细菌浮游生物的两个样本中海洋群 1 古菌（MG1C）的相对丰度（原核生物的 1.8%）升高。我们分析了这些样本中宏转录组中 MG1C 序列，以深入了解在环境中生长的 MG1C 种群的代谢情况，并与同一样本中的氨氧化细菌（AOB）进行比较。组装结果表明，大多数个体 MG1C 开放阅读框（ORF）的序列内多样性较低，与“Candidatus Nitrosopumilus maritimus”菌株 SCM1 基因组序列高度同源。与氨摄取和氧化相关的 ORF 读取占所有 MG1C 转录本的 37%。我们没有从用于氨吸收和氧化的 ORFs 中恢复任何读取，这些读取被提议用于编码替代的亚硝酰基氨氧化途径的组成部分；然而，大量出现了 Nmar_1259 和 Nmar_1667 的读取，这些读取被注释为编码与 nirK 同源的多铜氧化酶。两个同源 ORF（Nmar_1201 和 Nmar_1547）的读取也很丰富，被注释为假定蛋白，这表明它们未知的功能对 MG1C 很重要。超氧化物歧化酶和过氧化物酶样转录物在 MG1C 转录物库中的丰度高于完整宏转录物库，这表明 MG1C 种群对氧化应激的反应增强。qPCR 表明 AOB 的丰度较低（原核生物的 0.0010%），我们在分配给 AOB 的转录本中没有发现与氨氧化相关的转录本，只有一个 RuBisCO 转录本，这表明它们没有对与 MG1C 种群相同的环境线索做出反应。
