Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

Area of Science:

• Microbiology
• Genomics
• Environmental Science

Background:

• Most microbial diversity remains uncultured, hindering physiological understanding.
• Genomic and environmental data offer indirect insights into uncultured microbes.
• Global abundance of uncultured microbial groups has been largely unassessed.

Purpose of the Study:

• To quantify the global abundance of uncultured microbial groups.
• To assess the culture bias in microbial surveys.
• To determine the ecological significance of uncultured microbes.

Main Methods:

• Analysis of 16S rRNA gene sequences from metagenome and metatranscriptome databases.
• Comparison of sequences from diverse environments to nearest cultured relatives.
• Quantification of uncultured microbial abundances using read depths.

Main Results:

• Uncultured microbial groups dominate most environments, except human-associated ones.
• Phylogenetically novel uncultured groups comprise significant portions of microbial communities (22%–87% genera to classes, 0%–64% phyla).
• Uncultured microbes may represent 81% of microbial cells (genera) and 25% (phyla), with higher representation in metatranscriptomes, indicating viability.

Conclusions:

• Cultured microbes are not representative of global microbial diversity.
• Uncultured microbes, particularly novel phyla, are numerically dominant in nonhuman environments.
• The physiology of uncultured microbes is critical for understanding Earth systems and ecosystem functions.