skip to main content


Search for: All records

Creators/Authors contains: "Zhang, L"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Free, publicly-accessible full text available December 9, 2025
  2. Free, publicly-accessible full text available December 9, 2025
  3. Free, publicly-accessible full text available August 1, 2025
  4. ABSTRACT

    Phage-plasmids are unique mobile genetic elements that function as plasmids and temperate phages. While it has been observed that such elements often encode antibiotic resistance genes and defense system genes, little else is known about other functional traits they encode. Further, no study to date has documented their environmental distribution and prevalence. Here, we performed genome sequence mining of public databases of phages and plasmids utilizing a random forest classifier to identify phage-plasmids. We recovered 5,742 unique phage-plasmid genomes from a remarkable array of disparate environments, including human, animal, plant, fungi, soil, sediment, freshwater, wastewater, and saltwater environments. The resulting genomes were used in a comparative sequence analysis, revealing functional traits/accessory genes associated with specific environments. Host-associated elements contained the most defense systems (including CRISPR and anti-CRISPR systems) as well as antibiotic resistance genes, while other environments, such as freshwater and saltwater systems, tended to encode components of various biosynthetic pathways. Interestingly, we identified genes encoding for certain functional traits, including anti-CRISPR systems and specific antibiotic resistance genes, that were enriched in phage-plasmids relative to both plasmids and phages. Our results highlight that phage-plasmids are found across a wide-array of environments and likely play a role in shaping microbial ecology in a multitude of niches.

    IMPORTANCE

    Phage-plasmids are a novel, hybrid class of mobile genetic element which retain aspects of both phages and plasmids. However, whether phage-plasmids represent merely a rarity or are instead important players in horizontal gene transfer and other important ecological processes has remained a mystery. Here, we document that these hybrids are encountered across a broad range of distinct environments and encode niche-specific functional traits, including the carriage of antibiotic biosynthesis genes and both CRISPR and anti-CRISPR defense systems. These findings highlight phage-plasmids as an important class of mobile genetic element with diverse roles in multiple distinct ecological niches.

     
    more » « less
    Free, publicly-accessible full text available June 19, 2025
  5. Free, publicly-accessible full text available April 22, 2025
  6. Free, publicly-accessible full text available May 18, 2025
  7. Free, publicly-accessible full text available March 11, 2025
  8. Free, publicly-accessible full text available February 28, 2025
  9. This paper characterizes the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A, showing that each stress results in impaired growth rates, altered GDGT-lipid profiles, and differences in transcriptomes and proteomes. 
    more » « less