Evidence for archaeal metabolism of D-amino acids in the deep marine sediments

The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. Microbial metabolism plays a key role in the recycling of organic matter in the deep marine sediments. D-amino acids (DAAs) and DAA-containing muropeptides, an important g...

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Published in:The Science of the total environment 2024-10, Vol.948, p.174723, Article 174723
Main Authors: Yu, Yang, Liu, Ning-Hua, Teng, Zhao-Jie, Chen, Yin, Wang, Peng, Zhang, Yu-Zhong, Fu, Hui-Hui, Chen, Xiu-Lan, Zhang, Yu-Qiang
Format: Article
Language:English
Subjects:
Candidatus Bathyarchaeota
Candidatus Lokiarchaeaota
Microbial metabolism
Peptidoglycan
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Summary:The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. Microbial metabolism plays a key role in the recycling of organic matter in the deep marine sediments. D-amino acids (DAAs) and DAA-containing muropeptides, an important group of organic matter in the deep marine sediments, are primarily derived from bacterial peptidoglycan decomposition. Archaea are abundant in the deep ocean microbiome, yet their role in DAA metabolism remains poorly studied. Here, we report bioinformatic investigation and enzymatic characterization of deep marine sedimentary archaea involved in DAA metabolism. Our analyses suggest that a variety of archaea, particularly the Candidatus Bathyarchaeota and the Candidatus Lokiarchaeaota, can metabolize DAAs. DAAs are converted into L-amino acids via amino acid racemases (Ala racemase, Asp racemase and broad substrate specificity amino acid racemase), and converted into α-keto acid via d-serine ammonia-lyase, whereas DAA-containing di−/tri-muropeptides can be hydrolyzed by peptidases (dipeptidase and D-aminopeptidase). Overall, this study reveals the identity and activity of deep marine sedimentary archaea involved in DAA metabolism, shedding light on the mineralization and biogeochemical cycling of DAAs in the deep marine sediments. [Display omitted] •A variety of archaea metabolize D-amino acids in the deep marine sediments•Candidatus Bathyarchaeota and Candidatus Lokiarchaeaota are the dominant groups•Amino acid racemase, d-serine ammonia-lyase and peptidase are the key enzymes•Archaea convert D-amino acids into L-amino acids and α-keto acid•Archaea can metabolize D-amino acids-containing di−/tri-muropeptidess
ISSN:0048-9697
1879-1026
1879-1026
DOI:10.1016/j.scitotenv.2024.174723