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Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.
International Microbiology ( IF 3.1 ) Pub Date : 2020-01-14 , DOI: 10.1007/s10123-020-00119-z
José Félix Aguirre-Garrido 1, 2 , Francisco Martínez-Abarca 2 , Daniel Montiel-Lugo 3 , Luis Mario Hernández-Soto 1 , Hugo Ramírez-Saad 4
Affiliation  

Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.

中文翻译:

元基因组学分析揭示了叠氮化处理对细菌群落结构的不同影响,方法是富集盐碱环境样品中存在的特定蓝细菌。

在田间条件下处理环境样品可能需要使用化学防腐剂,尽管使用有时会导致微生物群落发生变化。叠氮化钠是一种常用的防腐剂,已知会差异地影响细菌的生长。通过部分16S rRNA基因焦磷酸测序评估,将叠氮化物和黑暗培养液应用于Isabel苏打湖水样品可引起细菌群落结构的变化。未经处理的水样品(WU)以γ-变形杆菌序列为主,占86%,而在经过叠氮化物处理(WA)的样品中,该组的丰度降低到33%,而与蓝细菌相关的序列则占53%。弹枪测序和基因组募集分析指出了Halomonas campanensis菌株LS21(基因组大小4.07 Mbp)和Synechococcus sp。RS9917(2.58 Mbp)是分别来自WA和WU环境库的序列读取的更高募集基因组,几乎涵盖了完整的基因组。用叠氮化钠和黑暗处理水样品的组合处理已证明对蓝细菌基团的选择性富集有效。这种方法可能允许根据不同来源的宏基因组DNA对蓝细菌进行完整(或几乎完整)的基因组测序,从而增加数据库中代表性不足的蓝细菌基因组的数量。
更新日期:2020-01-14
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