Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.

微生物真核生物是自然微生物群落不可或缺的组成部分，它们的纳入对于许多生态系统研究至关重要，但是大多数已发表的元基因组分析都忽略了真核生物。为了将真核生物包括在环境研究中，我们提出了一种从复杂的宏基因组学样本中回收真核生物基因组的方法。基因组恢复的关键步骤是分离真核和原核片段。我们开发了一个ķ-mer的基于策略的EukRep用于真核生物序列鉴定，并将其应用于环境样品中，以证明其能够进行基因组恢复，基因组完整性评估和代谢潜能预测。我们使用这种方法来测试添加有机碳对与间歇泉相关的微生物群落的影响，并检测了群落代谢的实质性变化，并针对几乎所有候选的门生细菌和古细菌以及真核生物进行了选择。重建了近乎完整的基因组，将三种真菌置于节肢动物和节肢动物体内。尽管碳固定之前，碳固定和硫氧化是间歇泉社区的重要功能，但有机碳受影响的社区显示出富含分泌的蛋白酶，分泌的脂肪酶，靶向CAZymes的纤维素，和甲醇氧化。通过从复杂的环境样本中重建和评估相对高质量的真菌，原生生物和轮虫基因组，我们证明了EukRep的广泛用途。这种方法为整个微生物群落的独立于栽培的分析开辟了道路。