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微生物方法很重要:使用叶片生物片的音声学数据集,识别微生物群破坏管道之间的差异

Brianne Palmer¹, Sabina Karačić², Gabriele Bierbaum²

¹Division of Paleontology Bonn Institute of Organismic Biology Nussallee 8, 53115 Bonn Germany.

Applications in plant sciences

|May 1, 2025

概括

生物信息管道的选择显著影响水生叶生物膜中的微生物群体分析. 对于16S和18SrRNA,建议使用DADA2,而Deblur为ITS测序提供了一个强大的替代方案.

科学领域:

微生物生态学微生物生态学
生物信息学是一种生物信息学.
古生物学的古生物学

背景情况:

水生巨化石上的微生物表明生物膜有助于保存.
要了解微生物对叶子保存的影响,需要对活植物和微生物安普利康序列的研究.
准确的数据解释取决于为微生物社区组成选择最佳的生物信息管道.

研究的目的:

为了比较三个生物信息管道 (DADA2,Deblur,UNOISE) 的性能,用于分析水生叶生物膜中的微生物群落.
评估不同无色化算法的对微生物群体组成估计的影响.
确定最适合用于分析16S rRNA,18S rRNA和ITS amplicon区域的管道.

主要方法:

从浮动和浸泡的叶子的生物膜的分析 *Nymphaea alba* 和 *Nuphar lutea*.
使用模拟社区来评估管道的准确性.
对16S核糖体RNA (rRNA),18S核糖体RNA和ITS片区域的原始剂的应用.
来自DADA2,Deblur和UNOISE管道的微生物社区组成的比较.

主要成果:

选择消毒管道会改变已识别的序列和特定类型的数量.
微生物群落在叶子深度 (浮动或潜水) 之间存在差异.
对微生物群落的环境影响因分析的片区域而异.

结论:

由于其在识别安普利康序列变异 (ASV) 方面的性能,建议DADA2用于分析16S rRNA和18S rRNA安普利康数据.
对于ITS地区,Deblur确定了最多的ASV,并显示了与DADA2的组成相似性,使其成为一个可行的选择.
管道选择对于在水生植物生物膜中准确地分析微生物群落至关重要.

关键词:

安普利康序列的测序方法生物信息学是一种生物信息学.拒绝使用,拒绝使用.叶子生物膜是一种生物膜.植物语法 (taphonomy) 是一种植物语法.

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