A detailed map of the microverse: Microbial niches

Date:
April 4, 2023
Source:
Friedrich-Schiller-Universitaet Jena
Summary:
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
research team has redefined microbial niches by determining which
microorganisms live together.


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FULL STORY ========================================================================== Whether in hot springs, in the human intestine or in the deep sea - - microorganisms colonise almost every place on earth, sometimes under
extreme conditions. Depending on how these organisms have adapted to the particular environmental conditions in such ecological niches, ecologists classify them as "generalists" or "specialists." 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 habitat 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 analysed 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 genome size 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 genome 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 genetic information 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 horizontal gene
transfer 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.

* RELATED_TOPICS
o Plants_&_Animals
# Nature # Microbes_and_More # Evolutionary_Biology #
Microbiology
o Earth_&_Climate
# Ecology # Environmental_Awareness # Environmental_Issues
# Earth_Science
* RELATED_TERMS
o Ecological_niche o Competitive_exclusion_in_ecology o
Ecological_succession o Environmental_impact_assessment o
Honey o Hip_dysplasia o Heritability o Microorganism

========================================================================== Story Source: Materials provided by
Friedrich-Schiller-Universitaet_Jena. Original written by Ute
Scho"nfelder. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, Bas E. Dutilh. A
social
niche breadth score reveals niche range strategies of generalists
and specialists. Nature Ecology & Evolution, 2023; DOI:
10.1038/s41559-023- 02027-7 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/04/230404114309.htm

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