Long-term dynamics in microbial eukaryotes communities: a paleolimnological view based on sedimentary DNA

Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, that were not previously considered in lacustrine sediment record analyses appeared to be potential biological markers of trophic status changes. Our data suggest that shifts in relative abundance of extant species, including shifts between rare and abundant taxa, drive ecosystem responses to local and global environmental changes. Community structure shift events were concomitant with major climate variations (more particularly in Lake Igaliku). However, this study shows that the impacts of climatic fluctuations may be overpassed by the high-magnitude eutrophication impacts, as observed in the eutrophicated Lake Bourget. Overall, our data show that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes.

评估湖泊生物多样性变化受人为活动或气候因子影响的程度，需要依赖大量古湖沼学（palaeolimnological）数据。本研究采用高通量测序（high-throughput sequencing）技术，基于两座湖泊——法国阿尔卑斯山布尔热湖（Lake Bourget）与格陵兰伊加利库湖（Lake Igaliku）的沉积DNA（sedimentary DNA）记录，构建了涵盖2200余年微生物真核生物（原生生物与真菌）多样性变化的时间序列数据。研究对176份沉积物样本进行测序，获得了大量微生物真核生物类群，共计得到16386个操作分类单元（operational taxonomic units, OTU），隶属于50个系统发育类群。因此，此前湖泊沉积记录分析中未被纳入考量的绿藻门（Chlorophyta）、甲藻纲（Dinophyceae）、定鞭藻纲（Haptophyceae）与纤毛虫门（Ciliophora）等微生物类群，或可作为营养状态变化的潜在生物标志物。本研究数据表明，现存物种的相对丰度变化——包括稀有类群与优势类群间的丰度转换——驱动着生态系统对局地与全球环境变化的响应。群落结构转变事件与重大气候变化事件同步出现，这一现象在伊加利库湖表现得尤为显著。然而本研究表明，正如在已发生富营养化的布尔热湖所观测到的那样，气候波动的影响可能会被高强度富营养化作用所盖过。综上，本研究数据证实，沉积物中保存的DNA是记录过去生物多样性变化的珍贵信息档案。