背景:RCA(玫瑰杆菌分支附属)簇属于玫瑰杆菌家族,代表温带至极地海洋中的主要玫瑰杆菌谱系。尽管它普遍存在和丰富,只有几个基因组和一个描述的物种,Planktomarinatemporata,存在。为了更深入地了解我们对该集群及其分类和功能多样性以及生物地理学的有限理解,我们从全球海洋中筛选了宏基因组数据集,并重建了隶属于该集群的宏基因组组装基因组(MAG).
结果:总共82个MAG,加上五个分离株的基因组,揭示了对基因组特征的意想不到的多样性和新颖的见解,功能多样性,并极大地完善了RCA集群的生物地理格局。该集群细分为三个属:Planktomarina,假浮游动物,和分支最深的念珠菌Paraplanktomarina。8种Planktomarina物种中的6种具有更大的基因组大小(2.44-3.12Mbp)和更高的GC含量(46.36-53.70%),42.22-43.72G+C%)。Cand.Paraplanktomarina仅由一个物种代表,基因组大小为2.40Mbp,GC含量为45.85%。根据原核基因组的SeqCode命名法,有效地描述了Planktomarina和Pseudoplanktomarina属的三个新物种。有氧缺氧光合作用(AAP)编码在三种Planktomarina物种中。出乎意料的是,蛋白视紫质(PR)在其他浮游生物和所有假浮游生物物种中编码,表明这种光驱动质子泵是获取RCA团簇互补能量的最重要模式。与Planktomarina物种相比,Pseudoplanktomarina物种在功能性状上表现出差异,并且适应了更多资源有限的条件。对不同物种的全球生物地理学的评估极大地扩展了发生的范围,并表明不同物种表现出不同的生物地理学模式。它们部分反映了物种的基因组特征。
结论:我们基于MAG的详细分析为多元化提供了新的思路,环境适应,和全球生物地理学的主要谱系的上层细菌。通过SeqCode命名法对RCA簇的主要属和种进行分类学划分和验证,可能是通过宏基因组学方法评估的海洋和其他原核群落中主要原核谱系和亚谱系的精细分类学鉴定的有希望的方法。视频摘要。
BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.
RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the
SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.
CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the
SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.