Li, Meng-Meng

ABSTRACT Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood–Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.

Abstract Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.

Abstract Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin–Benson–Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.