Uncovering novel functions of the enigmatic, abundant, and active <i>Anaerolineae</i> in a salt marsh ecosystem

<i>Anaerolineae</i>, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel <i>Anaerolineae</i> metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing <i>Anaerolineales</i>, <i>Promineifilales</i>, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and <i>Caldilineales</i> orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all <i>Anaerolineae</i> encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of <i>Anaerolineae</i> expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh <i>Anaerolineae</i> in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, <i>Anaerolineae</i> are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that <i>Anaerolineae</i> are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, <i>Anaerolineae</i> encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of <i>Anaerolineae</i> appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.