Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F23%3A00576651" target="_blank" >RIV/61388971:_____/23:00576651 - isvavai.cz</a>

Alternative codes found

RIV/60076658:12310/23:43907197

Result on the web

<a href="https://journals.asm.org/doi/10.1128/spectrum.01112-23" target="_blank" >https://journals.asm.org/doi/10.1128/spectrum.01112-23</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1128/spectrum.01112-23" target="_blank" >10.1128/spectrum.01112-23</a>

Result language

angličtina

Original language name

Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota

Original language description

Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes, however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments.IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.

Czech name

—

Czech description

—

Type

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

CEP classification

—

OECD FORD branch

10606 - Microbiology

Project

<a href="/en/project/GX19-28778X" target="_blank" >GX19-28778X: Phototrophic Gemmatimonadetes (PhotoGemm+)</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

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

Name of the periodical

Microbiology Spectrum

ISSN

2165-0497

e-ISSN

2165-0497

Volume of the periodical

11

Issue of the periodical within the volume

5

Country of publishing house

US - UNITED STATES

Number of pages

23

Pages from-to

e0111223

UT code for WoS article

001107303900059

EID of the result in the Scopus database

2-s2.0-85175828641