Metagenome-assembled genomes uncover a global brackish microbiome
Metagenome-assembled genomes uncover a global brackish microbiome
复制标题
DOI：
10.1186/s13059-015-0834-7
复制
发表时间：
2015-12-14
期刊：
影响因子：
12.3
通讯作者：
Andersson, Anders F.
中科院分区：
文献类型：
--
作者：
Hugerth, Luisa W.;Larsson, John;Andersson, Anders F.
背景：微生物是海洋和湖泊生物地球化学循环的主要驱动力。虽然基因组是理解生物体代谢、生态和进化的基础，但浮游细菌基因组的测序很少，部分原因是培养它们很困难。结果：我们利用自动分箱技术从波罗的海（世界上最大的半咸淡水水体之一）的宏基因组时间序列中重建了大量浮游细菌基因组。这些基因组代表了典型淡水和海洋进化枝中的新物种，包括以前未测序的进化枝。基因组的季节性动态遵循系统发育模式，但具有细粒度的谱系特异性变化，反映在基因含量上。流线型的迹象在大多数基因组中是明显的，估计的基因组大小与过滤器大小部分的丰度变化相关。将基因组与全球分布的宏基因组进行比较，发现来自北美咸淡水的片段招募具有高序列同一性，但来自湖泊或海洋的片段招募较少。这表明，在10万年前，早在波罗的海形成（8000年前）之前，就存在一个全球咸淡水元群落，其种群从淡水和海洋亲属中分化出来。这与波罗的海大多数多细胞生物形成鲜明对比，后者是适应当地环境的淡水或海洋生物。结论：我们描述了由宏基因组组装的大量新的浮游细菌基因组的基因含量、时间动态和生物地理。我们认为，微咸环境施加了如此强的选择，以至于适应它们的谱系在全球范围内蓬勃发展，而周围水生群落的影响有限。
Background: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them.Results: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts.Conclusions: We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.