Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
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DOI：
10.1093/gigascience/giaa053
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发表时间：
2020-06-01
期刊：
影响因子：
9.2
通讯作者：
Brown, Bonnie L.
中科院分区：
文献类型：
--
作者：
Reddington, Kate;Eccles, David;Brown, Bonnie L.
背景：河流生态系统是生物地球化学的发电站，主要由栖息在水柱和沉积物中的微生物群落驱动。由于河流被广泛用于人类目的（饮用水，娱乐，农业和工业），因此了解这些活动如何影响河流微生物群落的组成是至关重要的。最近的研究表明，河流宏基因组差异很大，这表明微生物群落数据应包括在大规模的河流生态系统模型。但这种生态基因组学研究还没有广泛应用于“水景”规模，很少有人应用最新的纳米孔技术。结果如下：我们使用MinION纳米孔测序研究了三大洲11条河流的宏基因组，这是一个便携式平台，可用于未来的全球河流监测。每次运行生成高达10 Gb的数据，平均读取长度为3.4 kb。在0.5-1.0的范围内完成了河流功能潜力的多样性和诊断。10（6）长读。我们对11条河流中的7条的观察结果与其他河流组学研究结果一致，我们在其他4条河流中发现了以前未被认识的微生物生物多样性。结论：更深层次的理解是，河流微生物财团和它们所履行的生态功能并不与地理位置相一致，而是涉及微生物对城市和其他人为影响的生态反应，并且在很短的地理空间内表现出类群的变化。
Background: Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad "aquascape" scale, and few if any have applied the newest nanopore technology. Results: We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0 . 10(6) long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers. Conclusions: Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.