Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes
Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes
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DOI：
10.1007/s00253-005-0228-y
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发表时间：
2006-08-01
影响因子：
5
通讯作者：
Tebbe, Christoph C.
中科院分区：
文献类型：
--
作者：
Fracchia, Letizia;Dohrmann, Anja B.;Tebbe, Christoph C.
细菌群落是堆肥生产中的重要催化剂。在这里，分析了成品堆肥中细菌的多样性是否稳定，并对生产过程具有特异性。单链构象多态性（SSCP）聚合酶链反应扩增的部分16S rRNA基因的基础上，被用来配置文件和分析从成品堆肥提取的总DNA中发现的细菌群落。不同批次的堆肥样品储存在一段时间的12年和1岁的蚯蚓堆肥进行了比较。根据数字图像分析，堆肥和蚯蚓粪的轮廓之间可以检测到明显的差异。三个不同时期的堆肥存储和复制蠕虫堆肥料堆之间的差异只有轻微的。通过DNA测序从SSCP图谱中共鉴定出41个不同的16S rRNA基因，其中绝大多数与尚未培养的细菌有关。从堆肥中检索到的序列主要属于放线菌门和厚壁菌门。与此相反，蚯蚓粪中主要是未培养的绿弯杆菌，酸杆菌，拟杆菌和芽单胞菌。用特异性基因探针和Southern印迹杂交强调差异。结果表明，不同的基质和堆肥过程中选择特定的细菌群落在成品。栖息在堆肥材料的细菌群落的特异性和一致性表明，培养独立的细菌群落分析是一个潜在的有用的指标，以表征成品堆肥的质量方面的生产过程和储存条件的影响。
Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.