Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences
Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences
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DOI：
10.1111/1462-2920.15112
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发表时间：
2020-07-29
影响因子：
5.1
通讯作者：
Konstantinidis, Konstantinos T.
中科院分区：
文献类型：
--
作者：
Rodriguez-R, Luis M.;Tsementzi, Despina;Konstantinidis, Konstantinos T.
测序技术和生物信息学管道的最新进展使得从不同环境中尚未访问尚未培养的微生物的基因组。但是，淡水基因组的目录仍然有限，大多数基因组恢复尝试中的大多数淡水生态系统尝试仅针对特定的分类单元。在这里，我们提出了一条结合了迭代减法套筒的基因组恢复管道，并将其应用于来自查塔胡奇河（美国东南部）的七个连接湖泊和河口的100个宏基因组数据集的时间序列。我们的一组元基因组组装基因组（MAG）代表> 400个尚未命名的基因组菌，大大增加了来自淡水湖泊的高质量MAG数量。我们提出了两个新型物种的名称：“ candidatuselulimicrobium humile'（“大约” Elulimicrobiota'，“ Patescibacteria”）和“ candidatusaquidulcis frankliniae”（“ glorofleflexi”）。在任何抽样点，我们的MAG总体代表了总微生物社区的一半。为了评估这些基因体在计时系列中的流行率，我们引入方法来估计相对丰度和栖息地的偏好，以控制不平衡的基因组质量和样本表示。我们证明了查塔胡奇湖中大多数基因组菌的高度栖息地特殊性和流行性。更广泛的生态范围表征了较小的基因组，其编码密度较高，这表明在国际化的分布中，总体优势更小，紧凑。
Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'CandidatusElulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'CandidatusAquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.