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Ecological and evolutionary implications of a mobile genetic element-rich haloarchaeon with unique osmotic resilience.

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Title: Ecological and evolutionary implications of a mobile genetic element-rich haloarchaeon with unique osmotic resilience.
Authors: Ni Y; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China., Bi W; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China., Yu H; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China., Chen L; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China., Yu Y; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China., Han J; Shanghai Wildlife and Protected Natural Areas Research Center, Shanghai, China., Wang Y; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
Source: Microbiology spectrum [Microbiol Spectr] 2026 Sep; Vol. 14 (9), pp. e0340325. Date of Electronic Publication: 2026 Jun 30.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: ASM Press Country of Publication: United States NLM ID: 101634614 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2165-0497 (Electronic) Linking ISSN: 21650497 NLM ISO Abbreviation: Microbiol Spectr Subsets: MEDLINE
Imprint Name(s): Original Publication: Washington, DC : ASM Press, 2013-
MeSH Terms: Halobacteriaceae*/genetics , Halobacteriaceae*/classification , Halobacteriaceae*/isolation & purification , Interspersed Repetitive Sequences*, Lakes/microbiology ; Plasmids/genetics ; Phylogeny ; Gene Transfer, Horizontal ; China ; Genome, Archaeal ; Salinity ; Osmotic Pressure ; Evolution, Molecular ; Adaptation, Physiological
Abstract: We isolated a novel halophilic archaeon, strain DSL9, representing the proposed new species Haloliberatus hailidukes gen. nov., sp. nov., from Dishui Lake, China. Unlike most obligate halophiles, DSL9 survives in low salinity, even distilled water, without lysis. Genomic analysis revealed dual salinity adaptation strategies: salt-in and compatible solutes, including a complete trehalose biosynthesis pathway. The strain harbors multiple plasmids, notably a 111,311 bp large plasmid (pHdsl9-3) encoding replication (Orc1/Cdc6, SSB), transcription (TFIIB), transmission (T4SS cluster, ArdC-like protein), and recombination (XerA) modules. pHdsl9-3 provides auxiliary functions such as defense, genome diversification, ion detoxification, and suggests active horizontal gene transfer. Similar elements are widespread in Halobacteriales, highlighting their role in haloarchaeal genetic diversity and plasticity. The encoded XerA hinted at a function beyond DNA dimer resolution, suggesting it may have been adapted by other archaeal mobile genetic elements. These findings underscore the need to investigate plasmid-driven evolution and environmental adaptation mechanisms in haloarchaea.IMPORTANCEThis study reports the isolation and characterization of DSL9, a novel halophilic archaeon from a freshwater lake. Remarkably, DSL9 defies the typical obligate halophilic lifestyle by surviving in low-salinity environments, including distilled water, without cell lysis. A key discovery is the identification of a 111,311 bp large plasmid harboring essential modules for replication, transcription, transmission, and integration. Widespread distribution of similar elements across Halobacteriales suggests their crucial role in haloarchaeal genetic diversity and plasticity, warranting further study of plasmid-mediated evolution and adaptation strategies.
Competing Interests: The authors declare no conflict of interest.
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Grant Information: 32370151 National Natural Science Foundation of China
Contributed Indexing: Keywords: halophilic archaeon; horizontal gene transfer; low salinity; megaplasmid
Entry Date(s): Date Created: 20260630 Date Completed: 20260902 Latest Revision: 20260903
Update Code: 20260903
PubMed Central ID: PMC13532300
DOI: 10.1128/spectrum.03403-25
PMID: 42379816
Database: MEDLINE
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  Label: Title
  Group: Ti
  Data: Ecological and evolutionary implications of a mobile genetic element-rich haloarchaeon with unique osmotic resilience.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AU" term="%22Ni+Y%22">Ni Y</searchLink>; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.<br /><searchLink fieldCode="AU" term="%22Bi+W%22">Bi W</searchLink>; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.<br /><searchLink fieldCode="AU" term="%22Yu+H%22">Yu H</searchLink>; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.<br /><searchLink fieldCode="AU" term="%22Chen+L%22">Chen L</searchLink>; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.<br /><searchLink fieldCode="AU" term="%22Yu+Y%22">Yu Y</searchLink>; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.<br /><searchLink fieldCode="AU" term="%22Han+J%22">Han J</searchLink>; Shanghai Wildlife and Protected Natural Areas Research Center, Shanghai, China.<br /><searchLink fieldCode="AU" term="%22Wang+Y%22">Wang Y</searchLink>; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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  Data: <searchLink fieldCode="JN" term="%22101634614%22">Microbiology spectrum</searchLink> [Microbiol Spectr] 2026 Sep; Vol. 14 (9), pp. e0340325. <i>Date of Electronic Publication: </i>2026 Jun 30.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22ASM+Press%22">ASM Press </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101634614 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>2165-0497 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2221650497%22">21650497 </searchLink><i>NLM ISO Abbreviation: </i>Microbiol Spectr <i>Subsets: </i>MEDLINE
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  Data: <i>Original Publication</i>: Washington, DC : ASM Press, 2013-
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  Data: <searchLink fieldCode="MM" term="%22Halobacteriaceae%22">Halobacteriaceae*</searchLink>/<searchLink fieldCode="MM" term="%22Halobacteriaceae+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Halobacteriaceae%22">Halobacteriaceae*</searchLink>/<searchLink fieldCode="MM" term="%22Halobacteriaceae+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Halobacteriaceae%22">Halobacteriaceae*</searchLink>/<searchLink fieldCode="MM" term="%22Halobacteriaceae+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Interspersed+Repetitive+Sequences%22">Interspersed Repetitive Sequences*</searchLink><br /><searchLink fieldCode="MH" term="%22Lakes%22">Lakes</searchLink>/<searchLink fieldCode="MH" term="%22Lakes+microbiology%22">microbiology</searchLink> ; <searchLink fieldCode="MH" term="%22Plasmids%22">Plasmids</searchLink>/<searchLink fieldCode="MH" term="%22Plasmids+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Phylogeny%22">Phylogeny</searchLink> ; <searchLink fieldCode="MH" term="%22Gene+Transfer%2C+Horizontal%22">Gene Transfer, Horizontal</searchLink> ; <searchLink fieldCode="MH" term="%22China%22">China</searchLink> ; <searchLink fieldCode="MH" term="%22Genome%2C+Archaeal%22">Genome, Archaeal</searchLink> ; <searchLink fieldCode="MH" term="%22Salinity%22">Salinity</searchLink> ; <searchLink fieldCode="MH" term="%22Osmotic+Pressure%22">Osmotic Pressure</searchLink> ; <searchLink fieldCode="MH" term="%22Evolution%2C+Molecular%22">Evolution, Molecular</searchLink> ; <searchLink fieldCode="MH" term="%22Adaptation%2C+Physiological%22">Adaptation, Physiological</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: We isolated a novel halophilic archaeon, strain DSL9, representing the proposed new species Haloliberatus hailidukes gen. nov., sp. nov., from Dishui Lake, China. Unlike most obligate halophiles, DSL9 survives in low salinity, even distilled water, without lysis. Genomic analysis revealed dual salinity adaptation strategies: salt-in and compatible solutes, including a complete trehalose biosynthesis pathway. The strain harbors multiple plasmids, notably a 111,311 bp large plasmid (pHdsl9-3) encoding replication (Orc1/Cdc6, SSB), transcription (TFIIB), transmission (T4SS cluster, ArdC-like protein), and recombination (XerA) modules. pHdsl9-3 provides auxiliary functions such as defense, genome diversification, ion detoxification, and suggests active horizontal gene transfer. Similar elements are widespread in Halobacteriales, highlighting their role in haloarchaeal genetic diversity and plasticity. The encoded XerA hinted at a function beyond DNA dimer resolution, suggesting it may have been adapted by other archaeal mobile genetic elements. These findings underscore the need to investigate plasmid-driven evolution and environmental adaptation mechanisms in haloarchaea.IMPORTANCEThis study reports the isolation and characterization of DSL9, a novel halophilic archaeon from a freshwater lake. Remarkably, DSL9 defies the typical obligate halophilic lifestyle by surviving in low-salinity environments, including distilled water, without cell lysis. A key discovery is the identification of a 111,311 bp large plasmid harboring essential modules for replication, transcription, transmission, and integration. Widespread distribution of similar elements across Halobacteriales suggests their crucial role in haloarchaeal genetic diversity and plasticity, warranting further study of plasmid-mediated evolution and adaptation strategies.
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: The authors declare no conflict of interest.
– Name: Ref
  Label: References
  Group: RefInfo
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  Group: Grant
  Data: 32370151 National Natural Science Foundation of China
– Name: SubjectMinor
  Label: Contributed Indexing
  Group:
  Data: <i>Keywords: </i>halophilic archaeon; horizontal gene transfer; low salinity; megaplasmid
– Name: DateEntry
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  Data: <i>Date Created: </i>20260630 <i>Date Completed: </i>20260902 <i>Latest Revision: </i>20260903
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  Data: 10.1128/spectrum.03403-25
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PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=cmedm&AN=42379816
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      – Type: doi
        Value: 10.1128/spectrum.03403-25
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        StartPage: e0340325
    Subjects:
      – SubjectFull: Lakes microbiology
        Type: general
      – SubjectFull: Plasmids genetics
        Type: general
      – SubjectFull: Phylogeny
        Type: general
      – SubjectFull: Gene Transfer, Horizontal
        Type: general
      – SubjectFull: China
        Type: general
      – SubjectFull: Genome, Archaeal
        Type: general
      – SubjectFull: Salinity
        Type: general
      – SubjectFull: Osmotic Pressure
        Type: general
      – SubjectFull: Evolution, Molecular
        Type: general
      – SubjectFull: Adaptation, Physiological
        Type: general
      – SubjectFull: Halobacteriaceae genetics
        Type: general
      – SubjectFull: Halobacteriaceae classification
        Type: general
      – SubjectFull: Halobacteriaceae isolation & purification
        Type: general
      – SubjectFull: Interspersed Repetitive Sequences
        Type: general
    Titles:
      – TitleFull: Ecological and evolutionary implications of a mobile genetic element-rich haloarchaeon with unique osmotic resilience.
        Type: main
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            – D: 01
              M: 09
              Text: 2026 Sep
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 2165-0497
          Numbering:
            – Type: volume
              Value: 14
            – Type: issue
              Value: 9
          Titles:
            – TitleFull: Microbiology spectrum
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