Abstract
BackgroundSequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases.ResultsOur results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4–86.3%) and 18.8% (9.1–52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa.ConclusionsThese results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions.EHyGD1bcuvyriCzccWszavVideo
Highlights
Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms
We evaluated the present situation of prokaryotic genome sequencing in the earth biomes for the first time
High genome-sequenced proportions in different prokaryotic biomes A representative subset, containing 10,000 samples to represent different environment types, was selected from 27,751 samples of 97 independent studies released by the Earth Microbiome Project (EMP) [13]
Summary
Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. The cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases. Genome sequencing provides a blueprint for the evolutionary and functional diversities of prokaryotes and improves our understanding of how they interact with one another, their hosts, and their surroundings [3,4,5]. Compared to the exponential accumulation of genomic data, the latest estimate of global prokaryotic operational taxonomic units (OTUs, 16S-V4 regions at 97% sequence identities) is only 0.8–1.6 million, far less than the trillions previously predicted [11, 12]. It is necessary to globally evaluate the proportion of sequenced prokaryotic genomes in environments
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