Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates.
Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates.
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DOI：
10.1186/s12915-022-01379-z
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发表时间：
2022-08-08
期刊：
影响因子：
5.4
通讯作者：
Scanlan, David J.
中科院分区：
文献类型：
--
作者：
Cabello-Yeves, Pedro J.;Callieri, Cristiana;Picazo, Antonio;Schallenberg, Lena;Huber, Paula;Roda-Garcia, Juan J.;Bartosiewicz, Maciej;Belykh, Olga, I;Tikhonova, Irina, V;Torcello-Requena, Alberto;De Prado, Paula Martin;Puxty, Richard J.;Millard, Andrew D.;Camacho, Antonio;Rodriguez-Valera, Francisco;Scanlan, David J.
蓝藻是主要的原核初级生产者，占据了世界范围内不同盐度水平的水生栖息地，使它们成为研究水生微生物学中未解决的主要难题之一的兴趣群体，这是区分海洋微生物和淡水微生物的原因。我们解决这个问题，使用生态基因组学的一组picocyanobacteria（集群5），最近已经发展到栖息在地理上不同的盐度小生境。我们的分析是通过对58个新的基因组进行测序而实现的，这些基因组来自这里介绍的这一组的淡水代表，代表了现有基因组数据的6倍增加。总体而言，淡水菌株具有较大的基因组（2.69 Mb和64%）和%GC含量（2.5 Mb和58.5%）相比，半咸水（2.69 Mb和64%）和海洋分离株。基因组的新颖性/盐度差异突出了海洋分离物中的酸性蛋白质组和特定的盐适应途径（例如，渗透物/相容性溶质-甘氨酸甜菜碱/ggp/gpg/gmg簇和甘油脂glpK/glpA），而淡水菌株具有不同的离子/钾通道、渗透酶（水通道蛋白Z）、脂肪酸去饱和酶和更多的中性/碱性蛋白质组。硫、氮、磷、碳（光合作用）或胁迫耐受性代谢，同时在栖息地之间显示出不同的基因组足迹，不同类型的传输器，并没有明显地转化为环境之间的主要功能差异。微咸水微生物表现出海洋（盐适应途径）和淡水特征的混合物，突出了它们的过渡性质。在营养状态偏好和遗传多样性方面，这里提供的过多的淡水分离物证实了它们在地球仪生态多样的沃茨定居的能力。此外，在淡水picocyanobacteria的基因组更大，更灵活/适应性的趋势可能暗示在更广泛的生态位在这种环境中相比，相对同质的海洋系统。在线版本包含补充材料，可通过10.1186/s12915-022-01379-z获得。
Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system. The online version contains supplementary material available at 10.1186/s12915-022-01379-z.
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