Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F19%3A00510068" target="_blank" >RIV/60077344:_____/19:00510068 - isvavai.cz</a>

Result on the web

<a href="https://www.nature.com/articles/s41396-019-0471-3.pdf" target="_blank" >https://www.nature.com/articles/s41396-019-0471-3.pdf</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/s41396-019-0471-3" target="_blank" >10.1038/s41396-019-0471-3</a>

Result language

angličtina

Original language name

Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

Original language description

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (Ca. Methylopumilus) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10606 - Microbiology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

The ISME Journal

ISSN

1751-7362

e-ISSN

—

Volume of the periodical

13

Issue of the periodical within the volume

11

Country of publishing house

GB - UNITED KINGDOM

Number of pages

14

Pages from-to

2764-2777

UT code for WoS article

000490275400012

EID of the result in the Scopus database

2-s2.0-85068911293