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Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria

Abstract

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood–Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b–3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.

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Fig. 1: Phylogenetic and evolutionary inference of actinobacterial MAGs.
Fig. 2: Overview of metabolic capabilities in three new actinobacterial classes.
Fig. 3: Maximum-likelihood phylogeny of concatenated AcsABC.
Fig. 4: Schematic view of proteins involved in homoacetogenesis.
Fig. 5: Evolution of CODH/ACS and hydrogenases in Actinobacteria.
Fig. 6: Laboratory enrichment of acetogenic Actinobacteria.
Fig. 7: Genome-resolved metabolic models in G55H and G55HB treatments.

Data availability

The MAGs described in this paper have been deposited under NCBI PRJNA649850 and the eLibrary of Microbial Systematics and Genomics, https://www.biosino.org/elmsg/index, under accession numbers LMSG_G000001169.1–LMSG_G000001505.1. Additional raw data that support the findings of this study are available from The National Omics Data Encyclopedia (https://www.biosino.org/node) under project OEP001752 and OEP001755.

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Acknowledgements

This study was supported by funding from the National Natural Science Foundation of China (Grant Nos 91951205, 91751206, 92051108, 32061143043, 31850410475, 31670009, and 31970122), the Natural Science Foundation of Guangdong Province, China (Grant No. 2016A030312003), Guangzhou Municipal People’s Livelihood Science and Technology Plan (Grant No. 201803030030), the U.S. National Science Foundation (DEB 1557042 and DEB 1841658), and Agricultural Science and Technology Innovation Project of the Chinese Academy of Agriculture Science (No. CAAS-ASTIP-2016-BIOMA). We thank Charlotte D. Vavourakis and Gerard Muyzer for providing the actinobacterial MAGs from metagenomes of soda lake sediments, and thank Xiao-Tong Zhang and Wen-Hui Lian for data collection. The authors would like to thank Wan Liu for the MAGs submission to the eLibrary of Microbial Systematics and Genomic (https://www.biosino.org/elmsg/index). The authors would also like to thank the Guangdong Magigene Biotechnology Co. Ltd., China, for NGS sequencing.

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W-JL and LC jointly conceived the study. LL, GW, E-MZ, and W-DX performed the sampling. J-YJ conceptualized the research goals under the supervision of W-JL and LC. Authors J-YJ, LL, Z-SH, and QZ performed the bioinformatics analyses. LL and J-YJ prepared the main figures. NS and AO wrote the nomenclature for the actinobacterial MAGs. LF, P-FL, and A-PL performed the enrichment experiments. J-YJ, LL, BPH, NS, AO, P-FL, B-ZF, H-CJ, RK, LC, and W-JL wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Lei Cheng or Wen-Jun Li.

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Jiao, JY., Fu, L., Hua, ZS. et al. Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria. ISME J (2021). https://doi.org/10.1038/s41396-021-00935-9

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