The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics
Autor: | Yanbin Yin, Huansheng Cao, Zhou Yang, Yohei Shimura, Jingrang Lu, Allen Joel, Masanobu Kawachi, Ferran Garcia-Pichel, Landon Jenkins, Morgan M. Steffen |
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Jazyk: | angličtina |
Rok vydání: | 2020 |
Předmět: |
water blooms
cyanobacterial bloom ecophysiology Ecology (disciplines) Niche Genomics Ecological and Evolutionary Science adaptation comparative genomics Biology Genome cyanobacteria Microbiology 03 medical and health sciences Virology metatranscriptome Microcystis aeruginosa Ecosystem 030304 developmental biology Comparative genomics 0303 health sciences 030306 microbiology Gene Expression Profiling Repertoire ecogenomics fungi genomic complexity Eutrophication QR1-502 Lakes Phenotype Metagenomics Evolutionary biology Adaptation Genome Bacterial Metabolic Networks and Pathways Research Article |
Zdroj: | mBio, Vol 11, Iss 3 (2020) mBio, Vol 11, Iss 3, p e01155-20 (2020) mBio |
ISSN: | 2150-7511 |
DOI: | 10.1128/mBio.01155-20 |
Popis: | 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. 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. |
Databáze: | OpenAIRE |
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