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首页> 外文期刊>Applied and Environmental Microbiology >Novel Bacterial Lineages at the (Sub)Division Level as Detected by Signature Nucleotide-Targeted Recovery of 16S rRNA Genes from Bulk Soil and Rice Roots of Flooded Rice Microcosms
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Novel Bacterial Lineages at the (Sub)Division Level as Detected by Signature Nucleotide-Targeted Recovery of 16S rRNA Genes from Bulk Soil and Rice Roots of Flooded Rice Microcosms

机译：从签名的核苷酸靶向从淹没的水稻微观世界的大块土壤和水稻根中回收16S rRNA基因而检测到的（亚）水平的新型细菌谱系

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Using a newly developed 16S rRNA gene (rDNA)-targeted PCR assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. For comparison, oxic rice roots were included as an additional sample in this investigation. The bacterial diversity detectable by this PCR assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (T-RFLP) analysis and comparative sequence analysis of cloned 16S rDNA. T-RFLP fingerprint patterns generated from rice roots contained 12 distinct terminal restriction fragments (T-RFs). In contrast, the T-RFLP fingerprint patterns obtained from the anoxic bulk soil contained 33 distinct T-RFs, a clearly higher level of complexity. A survey of 176 bulk soil 16S rDNA clone sequences permitted correlation of 20 T-RFs with phylogenetic information. The other 13 T-RFs remained unidentified. The predominant T-RFs obtained from rice roots could be assigned to members of the genus Pirellulawithin the Planctomycetales, while most of the T-RFs obtained from the bulk soil corresponded to novel lines of bacterial descent. Using a level of 16S rDNA sequence dissimilarity to cultured microorganisms of approximately 20% as a threshold value, we detected 11 distinct bacterial lineages for which pure-culture representatives are not known. Four of these lineages could be assigned to the orderPlanctomycetales, while one lineage was affiliated with the division Verrucomicrobia and one lineage was affiliated with the spirochetes. The other five lineages either could not be assigned to any of the main lines of bacterial descent or clearly expanded the known diversity of division level lineages WS3 and OP3. Our results indicate the presence of bacterial diversity at a subdivision and/or division level that has not been detected previously by the so-called universal 16S rDNA PCR assays.
机译：使用新开发的16S rRNA基因（rDNA）靶向PCR检测方法，对拟南芥属具有拟议的群体特异性，我们检查了淹没水稻微观世界的缺氧大块土壤中是否存在新颖的拟南芥样多样性。为了进行比较，在此研究中将有氧稻根作为额外样品包括在内。通过使用包括末端限制性片段长度多态性（T-RFLP）分析和克隆的16S rDNA的比较序列分析在内的组合方法，可以评估通过此PCR测定法可检测到的细菌多样性。从稻根产生的T-RFLP指纹图谱包含12个不同的末端限制性片段（T-RFs）。相反，从缺氧的块状土壤中获得的T-RFLP指纹图谱包含33种不同的T-RF，复杂程度明显更高。一项对176块土壤的16S rDNA克隆序列的调查允许将20个T-RF与系统发育信息相关联。其他13个T-RF仍未确定。从稻根获得的主要T-RFs可被分配给 Planctomycetales 内的 Pirellula 属，而从散装土壤中获得的大多数T-RF对应于细菌下降的新系。使用与大约20％的培养微生物的16S rDNA序列差异水平作为阈值，我们检测到11个不同的细菌谱系，而纯培养物的代表未知。这些谱系中的四个谱系可以被分配给 Planctomycetales ，而一个谱系与 Verrucomicrobia 分支相关，一个谱系与螺旋体相关。其他五个世系要么不能分配给任何细菌世系的主系，要么显然扩展了分裂级世系WS3和OP3的已知多样性。我们的结果表明，在以前未通过所谓的通用16S rDNA PCR分析检测到的细分和/或分区水平上，存在细菌多样性。

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