Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment
Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment
复制标题
DOI：
10.1186/s40168-018-0607-0
复制
发表时间：
2018-12-07
期刊：
影响因子：
15.5
通讯作者：
Murrell, J. Colin
中科院分区：
文献类型：
--
作者：
Carrion, Ornella;Larke-Mejia, Nasmille L.;Murrell, J. Colin
背景每年大约有500 Tg的异戊二烯排放到大气中，其量与甲烷的量相似，尽管其对气候的显著影响，但对异戊二烯在环境中的生物降解知之甚少。异戊二烯降解剂在分子水平上的分离和表征已经允许开发针对编码异戊二烯单加氧酶的-亚基的isoA的探针。这种酶属于可溶性二铁中心单加氧酶家族，催化异戊二烯降解途径的第一步。使用针对关键代谢基因的探针是分子生态学中研究复杂环境中特定细菌群的成功方法。在这里，我们开发和测试了一种新的isoA PCR引物集研究的分布，丰度和多样性的异戊二烯降解剂在广泛的environments.ResultsThe新的isoA探针特异性扩增isoA基因从分类上不同的异戊二烯降解细菌，包括成员的属红球菌，Variovorax，和Sphingopyxis。与编码非异戊二烯降解物相关加氧酶的基因没有交叉反应性。从富含异戊二烯的环境样品中提取的DNA的isoA扩增子的测序显示，大多数环境测试窝藏了相当多的各种isoA序列，白杨叶富集含有更多的遗传多样性isoA基因。使用这些isoA探针通过qPCR进行的定量显示，异戊二烯降解剂广泛存在于叶圈、陆地、淡水和海洋环境中。具体而言，土壤中的高异戊二烯排放的树木附近的异戊二烯降解bacterias.ConclusionThis研究提供了分子生态学的工具，以扩大我们的知识的分布，丰富和多样性的异戊二烯降解剂在环境中，这是一个基本的步骤，必须评估的影响，微生物在减轻这种重要的气候活性气体的影响。
BackgroundApproximately 500Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the -subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments.ResultsThe new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria.ConclusionThis study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.