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Background <p>The phylum <i>Candidatus</i> Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, <i>Candidatus</i> Cloacimonadia. Furthermore, the diversity and metabolic characteristics of <i>Candidatus</i> Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum <i>Candidatus</i> Cloacimonadota require further investigation.</p> Results <p>In this study, six high-quality metagenome-assembled genomes (MAGs) of <i>Candidatus</i> Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 <i>Candidatus</i> Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. <i>Candidatus</i> Cloacimonadota is widely distributed across diverse environments worldwide, and its class, <i>Candidatus</i> Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)–[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.</p> Conclusion <p>This study enhances the understanding of the diversity, metabolic potential, and global distribution of <i>Candidatus</i> Cloacimonadota<i>.</i> We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.</p>

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Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月5日

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  • Yi Liu,
  • Min Yu,
  • Xing Chen,
  • Lingman Ran,
  • Xiao-Hua Zhang

摘要

Background

The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.

Results

In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)–[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.

Conclusion

This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.