细胞外DNA在土壤和沉积物中普遍存在,并构成水生系统中环境DNA的主要部分。理论上,胞外DNA由基因组元件组成,这些基因组元件在陆地上发生的过程产生的不同程度的保存,在水柱和沉积物中。细胞外DNA可以作为营养来源,被微生物排泄或降解,或者吸附在矿物基质上,从而潜在地保存来自过去环境的信息。为了测试细胞外DNA是否记录湖相条件,我们从铁质Towuti湖的缺氧沉积物中依次提取了细胞外和细胞内DNA,印度尼西亚。我们对这两个部分应用了16SrRNA基因Illumina测序,以区分沉积物中外源和内源来源的细胞外DNA。环境序列仅在沉积物中作为细胞外DNA发现,起源于多种来源。例如,放线菌,Verrucomicrobia,和来自流域土壤的酸性细菌。水柱中初级生产力有限,导致氧化区蓝藻序列很少,而水体的分层主要导致好氧和厌氧异养生物的二次生产。氯氟菌和普兰切菌,水-沉积物界面下沉有机质和浮游序列的主要降解物,在埋葬的初始阶段优先保存。为了追踪细胞外DNA的内源性来源,我们使用细胞内DNA中分类群的相对丰度来定义哪些微生物种群生长,随着沉积物深度的增加,低密度下降或持续。细胞裂解成为细胞外DNA的重要额外来源,随着其他微生物属的深度越来越丰富,逐渐覆盖了以前的遗传组合。活性微生物使用细胞外DNA作为营养素导致选择性去除GC含量最低的序列。我们得出的结论是,保存在浅层湖相沉积物中的细胞外DNA反映了最初的环境背景,但逐渐被修改,从而从其地层背景转变。区分细胞外DNA的外源和内源来源可以同时解决湖内和沉积后的过程。在更深的沉积物中,如果以古DNA为目标,则细胞裂解的静止阶段和序列的积累将需要严格的提取和特定的引物。
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.