Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota

Jie Pan; Zhichao Zhou; Oded Béjà; Mingwei Cai; Yuchun Yang; Yang Liu; Ji Dong Gu; Meng Li

doi:10.1186/s40168-020-00820-1

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota

Jie Pan, Zhichao Zhou, Oded Béjà, Mingwei Cai, Yuchun Yang, Yang Liu, Ji Dong Gu, Meng Li^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

Background: Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Results: In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup. Conclusions: The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. [MediaObject not available: see fulltext.].

Original language	English
Article number	43
Journal	Microbiome
Volume	8
Issue number	1
DOIs	https://doi.org/10.1186/s40168-020-00820-1
State	Published - 31 Mar 2020
Externally published	Yes

Keywords

Bathyarchaeota
Calvin-Benson-Bassham cycle
Microoxic lifestyle
Porphyrin biosynthesis
Rhodopsin
Trimethylamine degradation
Urea producing

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10.1186/s40168-020-00820-1

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title = "Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota",

abstract = "Background: Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Results: In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup. Conclusions: The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. [MediaObject not available: see fulltext.].",

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author = "Jie Pan and Zhichao Zhou and Oded B{\'e}j{\`a} and Mingwei Cai and Yuchun Yang and Yang Liu and Gu, {Ji Dong} and Meng Li",

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doi = "10.1186/s40168-020-00820-1",

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AU - Pan, Jie

AU - Zhou, Zhichao

AU - Béjà, Oded

AU - Cai, Mingwei

AU - Yang, Yuchun

AU - Liu, Yang

AU - Gu, Ji Dong

AU - Li, Meng

PY - 2020/3/31

Y1 - 2020/3/31

N2 - Background: Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Results: In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup. Conclusions: The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. [MediaObject not available: see fulltext.].

AB - Background: Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Results: In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup. Conclusions: The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. [MediaObject not available: see fulltext.].

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KW - Calvin-Benson-Bassham cycle

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KW - Trimethylamine degradation

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Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota

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Keywords

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