Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential
Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage i...
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2025-06-01
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| author | Boxuan Deng Raoqiong Che Pinxin Zhu Yongxia Wang Zhiying Li Shiying Zhang Wei Xiao |
| author_facet | Boxuan Deng Raoqiong Che Pinxin Zhu Yongxia Wang Zhiying Li Shiying Zhang Wei Xiao |
| author_sort | Boxuan Deng |
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| description | Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. <i>Limnohabitans</i>, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting <i>Limnohabitans</i> have been reported to date. Here, we describe, for the first time, three phages infecting <i>Limnohabitans</i>, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on <i>Limnohabitans</i> in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding <i>Limnohabitans</i>–phage interactions. |
| format | Article |
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| institution | Kabale University |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-cee2dc8bd8d44335bd95281f0edd290b2025-08-20T03:29:35ZengMDPI AGMicroorganisms2076-26072025-06-01136132410.3390/microorganisms13061324Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic PotentialBoxuan Deng0Raoqiong Che1Pinxin Zhu2Yongxia Wang3Zhiying Li4Shiying Zhang5Wei Xiao6Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650500, ChinaYunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650500, ChinaYunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650500, ChinaYunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650500, ChinaYunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650500, ChinaYunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, ChinaYunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650500, ChinaBacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. <i>Limnohabitans</i>, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting <i>Limnohabitans</i> have been reported to date. Here, we describe, for the first time, three phages infecting <i>Limnohabitans</i>, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on <i>Limnohabitans</i> in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding <i>Limnohabitans</i>–phage interactions.https://www.mdpi.com/2076-2607/13/6/1324<i>Limnohabitans</i>bacteriophagegenomedistributionauxiliary metabolic genes |
| spellingShingle | Boxuan Deng Raoqiong Che Pinxin Zhu Yongxia Wang Zhiying Li Shiying Zhang Wei Xiao Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential Microorganisms <i>Limnohabitans</i> bacteriophage genome distribution auxiliary metabolic genes |
| title | Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential |
| title_full | Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential |
| title_fullStr | Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential |
| title_full_unstemmed | Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential |
| title_short | Genome Sequences of the First Phages Infecting <i>Limnohabitans</i> Reveal Their Global Distribution and Metabolic Potential |
| title_sort | genome sequences of the first phages infecting i limnohabitans i reveal their global distribution and metabolic potential |
| topic | <i>Limnohabitans</i> bacteriophage genome distribution auxiliary metabolic genes |
| url | https://www.mdpi.com/2076-2607/13/6/1324 |
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