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Updated: Dec 6, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.

Yi Yang¹, Yaozhi Zhang^1,2, Natalie L Cápiro³

¹Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.

Frontiers in Microbiology

|October 5, 2020

Summary

Dehalococcoidia (Dia) microorganisms cluster into terrestrial and two marine groups. Marine Dia show more horizontal gene transfer and distinct metabolic enzymes, suggesting varied roles in element cycling.

Keywords:

Dehalococcoidia evolution genome comparison reductive dehalogenase time tree

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Area of Science:

Microbial genomics
Evolutionary biology
Environmental microbiology

Background:

Dehalococcoidia (Dia) are widespread microorganisms found in diverse environments.
Previous studies using MAGs and SAGs advanced understanding of Dia ecology and evolution.
A comprehensive genomic and evolutionary analysis across distinct geographical distributions is lacking.

Purpose of the Study:

To investigate the genomic and evolutionary characteristics of Dehalococcoidia (Dia) across different environments.
To analyze metabolic traits and evolutionary patterns of Dia microorganisms using available genomic data.

Main Methods:

Phylogenetic analysis of 16S rRNA genes from sixty-seven Dia genomes.
Comparative genomic analysis, including pangenome analysis.
Identification of horizontally transferred genetic materials and cluster-specific enzymes.

Main Results:

Dia microorganisms were classified into three phylogenetic groups: terrestrial (Dehalococcoides, Dehalogenimonas), marine cluster I, and marine cluster II.
Marine Dia clusters exhibited a higher proportion of horizontally transferred genes compared to the terrestrial cluster.
Cluster-specific enzymes (e.g., dehalogenase in terrestrial, sulfite reductase in marine) and biosynthesis pathways (e.g., siroheme in marine) were identified.

Conclusions:

Genomic divergence between marine and terrestrial Dia suggests distinct functional roles in biogeochemical cycling (carbon, sulfur, chlorine).
Marine Dia possess versatile metabolic capabilities beyond organohalide respiration, indicating adaptation to varied energy conservation strategies.
Further interdisciplinary research is needed to fully elucidate the physiology and evolution of Dia in diverse ecosystems.