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
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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DOI：
10.1128/aem.67.2.623-631.2001
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发表时间：
2001-02-01
影响因子：
4.4
通讯作者：
Liesack, W
中科院分区：
文献类型：
--
作者：
Derakshani, M;Lukow, T;Liesack, W
使用新开发的16 S rRNA基因（rDNA）为靶向的PCR检测与建议的组特异性的浮游菌，我们研究了缺氧散装土壤的淹没水稻微宇宙的存在下，新的浮游菌样的多样性。为了比较，在本次调查中，好氧水稻根作为一个额外的样品。利用末端限制性片段长度多态性（T-RFLP）分析和克隆的16 S rDNA序列比较分析相结合的方法，对该PCR方法检测到的细菌多样性进行了评价。相比之下，从缺氧的散装土壤中获得的T-RFLP指纹图谱包含33个不同的T-RFs，一个明显更高的复杂性水平。176块土壤16 S rDNA克隆序列的调查允许20 T-RFs与系统发育信息的相关性。其他13个T-RF仍未查明。从水稻根中获得的占主导地位的T-RFs可以被分配到Pirellula属的浮游菌目内的成员，而大部分的T-RFs从散装土壤中获得对应的细菌血统的新线路。使用水平的16 S rDNA序列相似性培养的微生物的约20%作为阈值，我们检测到11个不同的细菌谱系，其中纯培养的代表是未知的。这些谱系中的四个可以被分配到浮游菌目，而一个谱系隶属于疣微菌科，一个谱系隶属于螺旋体。其他五个谱系要么不能被分配到任何细菌血统的主线，要么明显扩展了已知的分裂水平谱系WS 3和OP 3的多样性。我们的研究结果表明，在细分和/或分裂的水平，还没有被检测到以前的所谓的通用16 S rDNA PCR检测的细菌多样性的存在。
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 Pirellula within 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 order Planctomycetales, 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.