Actinobacteria might contribute to microbial carbon neutral

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Carbon fixation by chemoautotrophic microbes had a major impact on the transition from the inorganic to the organic world, and could contribute to carbon neutral. Classically, it was thought that only a few autotrophic lineages could take part in this process, and Actinobacteria always been overlooked. In early 2018, our laboratories found that there were several actinobacterial MAGs from hot springs containing the gene sets for Wood–Ljungdahl pathway (WLP), and Vavourakis et al. also provided the gene evidence for actinobacterial WLP [1]. These results let us consider that WLP might be more prevalent than we know in Actinobacteria, and they might be members for carbon fixation. Considering there is no evidence showing that the Actinobacteria could use WLP for carbon fixation, and the diversity of actinobacterial WLP is still unknown, we thus studied autotrophy in Actinobacteria and the evolutionary history of actinobacterial WLP.

First, we decided to comprehensively investigate the WLP in Actinobacteria. We downloaded all the genomes of uncultivated Actinobacteria from NCBI, and found WLP was prevalent in three novel lineages. After that, we established a database of actinobacterial MAGs with WLP, which was used for searching the genomes belong to these three novel classes from our local hot spring metagenomic dataset and public databases. To our surprise, more than 40 MAGs were obtained and most of which contained genes for WLP. We named these three novel classes ‘Ca. Geothermincolia’, ‘Ca. Humimicrobiia’, ‘Ca. Aquicultoria’. Our analysis revealed functional differences among the three classes, but their common characteristics (WLP enzymes, hydrogenases, and enzymes for generating acetate) give us confidence that they might be homoacetogens – a property not known to exist in Actinobacteria. Further, we designed enrichment experiments, and fortunately, the relative abundance of ‘Ca. Geothermincolia’ in treatments with H2 and CO2 is much higher than the treatments without H2 and CO2, which is consistent with the proposed homoacetogenic metabolism. After analyzing their genomes, we performed the evolutionary analysis, and we thought about with luck – the actinobacterial WLP is quite important for the evolutionary of WLP, and the Actinobacteria likely donated genes for CODH/ACS to multiple lineages, such as the Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria.

Illustration credit: Yu-Zhen Ming from Wen-Jun Li's group at School of Life Sciences, Sun Yat-Sen University

In retrospect, these findings indicate that Actinobacteria might contribute to microbial carbon neutral from two aspects: Actinobacteria might process carbon fixation through WLP, and likely donated CODH/ACS genes to multiple lineages. Initially, the interesting thing about the actinobacterial WLP attracted our attention, and surprisingly, function analysis showed a new aspect of Actinobacteria. As it often happens, an interesting discovery will become the main motivation for research. Sometimes, one simply needs to stay curious and keep eyes open, you will find the 'colorful' side of the microbial world.

1. Vavourakis, C. D., Andrei, A. S., Mehrshad, M., Ghai, R., Sorokin, D. Y., & Muyzer, G. (2018). A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome, 6(1), 1-18. https://doi.org/10.1186/s40168-018-0548-7

Check out the full story in The ISME Journal: https://www.nature.com/articles/s41396-021-00935-9

Jian-Yu Jiao

Postdoc, Sun Yat-Sen University