Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements

Area of Science:

• Microbiology
• Genetics
• Environmental Science

Background:

• Anaerobic methane-oxidizing archaea, such as Methanoperedens, play a crucial role in mitigating methane emissions.
• Extrachromosomal genetic elements (ECEs), including large Borgs, are known to exist in Methanoperedens and may affect their activity.
• The diversity and impact of Methanoperedens ECEs beyond Borgs remain largely unexplored.

Purpose of the Study:

• To investigate the diversity of extrachromosomal genetic elements (ECEs) in Methanoperedens.
• To characterize newly identified ECEs, including linear elements, viruses, and circular elements.
• To understand the potential interactions and evolutionary impact of these ECEs on their archaeal hosts.

Main Methods:

• Bioinformatic analysis of genomic data from Methanoperedens.
• Identification and characterization of novel linear ECEs, circular viruses, and other unclassified ECEs.
• Comparative analysis of genetic features, including shared proteins and coding patterns, with known Borgs and Methanoperedens.

Main Results:

• Discovery of small linear ECEs, termed mini-Borgs (52–145 kb), sharing features with Borgs but distinct in size.
• Identification of eight families of Methanoperedens viruses, some encoding multi-haem cytochromes.
• Characterization of circular ECEs with transposon-associated genes and CRISPR arrays, indicating genetic exchange.

Conclusions:

• Mini-Borgs represent a new class of ECEs in Methanoperedens, genetically diverse and potentially influencing host activity.
• The identified viruses and circular ECEs contribute to the complex genetic landscape within Methanoperedens.
• Evidence suggests significant genetic information exchange between these ECEs and their Methanoperedens hosts, impacting archaeal evolution.