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Bioinformatician presents the first map of the microverse

The first map of the microverse
A diverse and global microbial dataset. a, Samples were received from vastly different annotated biomes and study designs. The numbers in parentheses indicate the number of samples within the annotated biome. Annotated biomes with fewer than 347 samples have been grouped as other. b, Geographical distribution of the samples. c, Total number of taxonomically annotated reads per sample (n = 22,518 samples). The box plot shows the interquartile range and median. No samples with fewer than 50,000 reads were selected. d, Samples from similar annotated biomes cluster together based on taxonomic profile in a t-SNE visualization (perplexity = 500), with the same ecological dissimilarity measure used as for SNB (namely, the Spearman’s rank correlation coefficient (0.5−(ρ/2)0.5−(ρ/2)0.5 - (\rho /2)) of known taxa at taxonomic rank order). Most samples from the plants biome were derived from seagrasses and macroalgae from kelp forests. e, Taxa richness differs per annotated biome and taxonomic rank. The low number of annotated species is a consequence of a relatively unexplored biosphere. su., superkingdom; p., phylum; c., class; o., order; f., family; g., genus; s., species. f, Annotated biomes with high mean α diversity have low β diversity, whereas both low and high β diversity is found among annotated biomes with low mean α diversity. freshw., freshwater; wetl., wetlands. Credit: Nature Ecology & Evolution (2023). DOI: 10.1038/s41559-023-02027-7

What defines the habitat—the ecological niche—of a microorganism? It is a combination of environmental factors such as temperature, moisture, and nutrient content. But the exact contribution of each of these factors is difficult to predict. A German-Dutch research team has redefined microbial niches by determining which microorganisms live together. Led by Prof. Dr. Bas E. Dutilh from the University of Jena and Utrecht University, the researchers present this "social niche breadth" approach in the current issue of the journal Nature Ecology & Evolution and use it to chart the first "Map of the Microverse".

Whether in , in the human intestine or in the deep sea—microorganisms colonize almost every place on earth, sometimes under . Depending on how these organisms have adapted to the particular environmental conditions in such ecological niches, ecologists classify them as "generalists" or "". While generalists can cope with a wide range of environmental conditions, specialists grow only under very specific circumstances.

"A key question for the study of such different microbial strategies is how to define microbial ecological niches in the first place," says Prof. Dr. Bas E. Dutilh. Until now, this has mainly been done based on subjective environmental parameters, which hardly allow unbiased quantification of the niche.

The bioinformatician from the Cluster of Excellence "Balance of the Microverse" at the University of Jena, together with researchers from Utrecht University, has therefore used a novel—data-driven—method to describe microbial niches, in which the species community itself is considered the decisive environmental factor instead of external conditions. This works because microbial communities adapt rapidly to their environment, so their composition reflects the sum of all environmental factors.

Most microbial habitats dominated by generalists

For their study, the researchers analyzed and quantified thousands of metagenomic data sets from different microbial samples from all over the world. "We found that in most habitats, generalists are dominant," says Dutilh. The researchers were initially surprised by this finding, as they had assumed that in local niches, specialists might prevail because they are better adapted to the particular conditions. But they found that competing generalists could grow much faster and thus gain dominance in the niche.

"For the generalists it's hit-or-miss, though; either they make it or they don't. This makes them quite variable in their presence. Specialists are more stable in their niche, albeit at low abundance."

And there was another result that the researchers had not expected: The genomes of the generalists are not particularly large. "This was previously assumed because metabolic flexibility was thought to generally require a larger genome," reports Dutilh. But as it turns out, the correlation between niche range and is more complex.

"We discovered two contrasting evolutionary strategies: In habitats with relatively low local biodiversity, such as animal-associated microbiomes, the specialists have a relatively small genome. In highly biodiverse habitats such as soils, the of the specialists is significantly larger."

The genomes of generalists are more variable than those of specialists, with genes coming and going during evolution. This allows them to integrate from other organisms through horizontal gene transfer and thus to adapt rapidly to the local niche. "We also see specific functions that are associated with in generalists' genomes," according to Dutilh.

The functions associated with specialists are much more diverse, often related to very specific metabolic processes. The genomes of specialists are evolutionarily stable, unlike those of generalists.

"In conclusion, our analysis sheds new and unexpected light on microbial niche range strategies throughout the microbial tree of life," Bas E. Dutilh is convinced.

More information: F. A. Bastiaan von Meijenfeldt et al, A social niche breadth score reveals niche range strategies of generalists and specialists, Nature Ecology & Evolution (2023). DOI: 10.1038/s41559-023-02027-7

Journal information: Nature Ecology & Evolution

Provided by University of Jena

Citation: Bioinformatician presents the first map of the microverse (2023, April 3) retrieved 23 September 2023 from
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