Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments
ABSTRACT Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putativ...
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American Society for Microbiology
2025-06-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.00705-25 |
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| author | Sheng-Xuan Peng Shao-Ming Gao Zhi-Liang Lin Zhen-Hao Luo Si-Yu Zhang Wen-Sheng Shu Fangang Meng Li-Nan Huang |
| author_facet | Sheng-Xuan Peng Shao-Ming Gao Zhi-Liang Lin Zhen-Hao Luo Si-Yu Zhang Wen-Sheng Shu Fangang Meng Li-Nan Huang |
| author_sort | Sheng-Xuan Peng |
| collection | DOAJ |
| description | ABSTRACT Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth’s prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system. |
| format | Article |
| id | doaj-art-a2ab64da14d14c2fa8341ac21705449e |
| institution | Kabale University |
| issn | 2150-7511 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj-art-a2ab64da14d14c2fa8341ac21705449e2025-08-20T03:46:50ZengAmerican Society for MicrobiologymBio2150-75112025-06-0116610.1128/mbio.00705-25Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sedimentsSheng-Xuan Peng0Shao-Ming Gao1Zhi-Liang Lin2Zhen-Hao Luo3Si-Yu Zhang4Wen-Sheng Shu5Fangang Meng6Li-Nan Huang7School of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaSchool of Life Sciences, South China Normal University, Guangzhou, Guangdong, ChinaSchool of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaABSTRACT Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth’s prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.https://journals.asm.org/doi/10.1128/mbio.00705-25microbial ecologyultramicrobacteriaDPANN archaeabiogeographyhost-cell interactions |
| spellingShingle | Sheng-Xuan Peng Shao-Ming Gao Zhi-Liang Lin Zhen-Hao Luo Si-Yu Zhang Wen-Sheng Shu Fangang Meng Li-Nan Huang Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments mBio microbial ecology ultramicrobacteria DPANN archaea biogeography host-cell interactions |
| title | Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments |
| title_full | Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments |
| title_fullStr | Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments |
| title_full_unstemmed | Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments |
| title_short | Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments |
| title_sort | biogeography and ecological functions of underestimated cpr and dpann in acid mine drainage sediments |
| topic | microbial ecology ultramicrobacteria DPANN archaea biogeography host-cell interactions |
| url | https://journals.asm.org/doi/10.1128/mbio.00705-25 |
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