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Sediment Metagenomes as Time Capsules of Lake Microbiomes
mSphere ( IF 4.8 ) Pub Date : 2020-11-04 , DOI: 10.1128/msphere.00512-20 Rebecca E Garner 1, 2 , Irene Gregory-Eaves 2, 3 , David A Walsh 2, 4
mSphere ( IF 4.8 ) Pub Date : 2020-11-04 , DOI: 10.1128/msphere.00512-20 Rebecca E Garner 1, 2 , Irene Gregory-Eaves 2, 3 , David A Walsh 2, 4
Affiliation
The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria (“Candidatus Nanopelagicales”) and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.
中文翻译:
沉积物宏基因组作为湖泊微生物组的时间胶囊
从湖泊沉积物档案中重建生态时间序列可以追溯人类活动对环境的影响。古湖泊学中的分子遗传学方法提供了前所未有的 DNA 时间序列,它记录了历史湖泊生态系统中微生物生态的证据。此类研究通常依赖于单基因调查,因此,保存的微生物的全部多样性仍未得到探索。在这项研究中,我们通过对加拿大东部三个湖泊的地表水和沉积物样本进行比较霰弹枪宏基因组分析,探讨了当代和工业化前沉积物的多样性。在一项旨在从本土沉积物背景中解开历史 DNA 的策略中,通过绘制沉积物宏基因组读数和参考地表水宏基因组组装之间的序列相似性来捕获微生物保存信号。我们检测到保存蓝藻、各种浮游细菌、微真核生物和沉积物宏基因组中的病毒。在保存的微生物中,有一些以前从未在古湖水学重建中报道过的重要群体,包括噬菌体(Caudovirales)和无处不在的淡水β变形杆菌(Polynucleobacter和Limnohabitans)。相比之下,超显微放线菌(“ Candidatus Nanopelagicales”) 和Alphaproteobacteria ( Pelagibacterales) 显然在沉积物宏基因组中保存得不好,尽管它们在地表水宏基因组中在数量上占主导地位。总体而言,我们的研究探索了全宏基因组鸟枪法测序的新应用,以发现保存在湖泊沉积物中的各种微生物的 DNA 残留物。不同微生物时间序列的恢复支持微生物组重建的分类扩展和新型微生物古指标的开发。
更新日期:2020-11-04
中文翻译:
沉积物宏基因组作为湖泊微生物组的时间胶囊
从湖泊沉积物档案中重建生态时间序列可以追溯人类活动对环境的影响。古湖泊学中的分子遗传学方法提供了前所未有的 DNA 时间序列,它记录了历史湖泊生态系统中微生物生态的证据。此类研究通常依赖于单基因调查,因此,保存的微生物的全部多样性仍未得到探索。在这项研究中,我们通过对加拿大东部三个湖泊的地表水和沉积物样本进行比较霰弹枪宏基因组分析,探讨了当代和工业化前沉积物的多样性。在一项旨在从本土沉积物背景中解开历史 DNA 的策略中,通过绘制沉积物宏基因组读数和参考地表水宏基因组组装之间的序列相似性来捕获微生物保存信号。我们检测到保存蓝藻、各种浮游细菌、微真核生物和沉积物宏基因组中的病毒。在保存的微生物中,有一些以前从未在古湖水学重建中报道过的重要群体,包括噬菌体(Caudovirales)和无处不在的淡水β变形杆菌(Polynucleobacter和Limnohabitans)。相比之下,超显微放线菌(“ Candidatus Nanopelagicales”) 和Alphaproteobacteria ( Pelagibacterales) 显然在沉积物宏基因组中保存得不好,尽管它们在地表水宏基因组中在数量上占主导地位。总体而言,我们的研究探索了全宏基因组鸟枪法测序的新应用,以发现保存在湖泊沉积物中的各种微生物的 DNA 残留物。不同微生物时间序列的恢复支持微生物组重建的分类扩展和新型微生物古指标的开发。