The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics
The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics
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DOI：
10.1128/mbio.01155-20
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发表时间：
2020-05-01
期刊：
影响因子：
6.4
通讯作者：
Garcia-Pichel, Ferran
中科院分区：
文献类型：
--
作者：
Cao, Huansheng;Shimura, Yohei;Garcia-Pichel, Ferran
水华的发展，由于富营养化构成的情况下，生态位专业化的浮游蓝藻，但基因组剧目允许水华形成只有一些物种还没有得到充分的表征。我们假设，一个性状的栖息地相关性产生了其潜在的基因组复杂性，因此，在该栖息地成功繁衍的物种中，与不能在该栖息地成功繁衍的相近物种相比，该谱系中的性状将更加复杂。为了测试水华蓝藻的情况下，我们策划了17个潜在的相关查询代谢途径和5个核心途径选择根据现有的生态生理学文献。将可用的113个基因组分成开花（45个）或非开花（68个）菌株，并推导出每个菌株的每个途径版本的基因组复杂性指数。我们发现，所有查询途径的菌株版本显着更复杂的开花，与复杂性实际上正相关的菌株开花的发病率在14个这些途径。五个核心途径，相关无处不在，没有表现出差异的复杂性或相关性。气泡，毒素和脂肪酸的合成，氨基酸的吸收，和C，N和S的收购系统是最显着相关的开花剧目。此外，我们验证了我们的研究结果，使用宏基因组基因表达分析开花和nonblooming蓝藻在自然环境中，在剧目中的途径差异过表达，根据其相对复杂的开花，但不是在nonbloomers。我们希望这种方法可以找到其他栖息地和organismal groups.IMPORTANCE的应用程序，我们务实地描绘的特征库，使生物生态位专业化。我们基于我们的方法的原则，从进化和复杂系统的考虑，基因组单位，可以显着有助于健身在一定的栖息地将相对更复杂的生物体专门的栖息地比他们的基因组同源物中发现的生物体从其他栖息地。我们在形成有害水华的蓝藻中测试了这一点，在生态生理学和基因组学方面存在数十年的努力。我们的研究结果基本上证实，基因组学和生态可以通过比较复杂性分析，提供了一种工具，应该是普遍适用于任何组的生物体和任何栖息地，并使接地的假设有关多样化的生态基因组学的基础。
Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes were split into those of blooming (45) or nonblooming (68) strains, and an index of genomic complexity for each strain's version of each pathway was derived. We show that strain versions of all query pathways were significantly more complex in bloomers, with complexity in fact correlating positively with strain blooming incidence in 14 of those pathways. Five core pathways, relevant everywhere, showed no differential complexity or correlations. Gas vesicle, toxin and fatty acid synthesis, amino acid uptake, and C, N, and S acquisition systems were most strikingly relevant in the blooming repertoire. Further, we validated our findings using metagenomic gene expression analyses of blooming and nonblooming cyanobacteria in natural settings, where pathways in the repertoire were differentially overexpressed according to their relative complexity in bloomers, but not in nonbloomers. We expect that this approach may find applications to other habitats and organismal groups.IMPORTANCE We pragmatically delineate the trait repertoire that enables organismal niche specialization. We based our approach on the tenet, derived from evolutionary and complex-system considerations, that genomic units that can significantly contribute to fitness in a certain habitat will be comparatively more complex in organisms specialized to that habitat than their genomic homologs found in organisms from other habitats. We tested this in cyanobacteria forming harmful water blooms, for which decades-long efforts in ecological physiology and genomics exist. Our results essentially confirm that genomics and ecology can be linked through comparative complexity analyses, providing a tool that should be of general applicability for any group of organisms and any habitat, and enabling the posing of grounded hypotheses regarding the ecogenomic basis for diversification.