Unveiling the carbon fixation potential of marine Prokaryotes using MarMAGs, a novel user-friendly database with over 130 thousand metagenome assemble genomes

Our team designed the MarMAGs, a user-friendly database containing over 130 thousand marine metagenome-assembled genomes (MAGs). Users can access this data from coordinates in a map or by filtering it based on its metadata (e.g., marine biome, biogeographic features, and sequencing platform). Further, we showcased carbon fixation as a use case.
We recovered metagenome-assembled genomes (MAGs) from 3405 marine metagenomes selected from MarineMetagenomeDB (https://web.app.ufz.de/marmdb/) and added 52162 MAGs from the OceanDNA dataset and 8558 marine MAGs from the GEM catalog. We evaluated genome quality, taxonomy, and assembly. After metadata harmonization, we identified the genes for prokaryotes' carbon fixation pathways that included the Reductive pentose phosphate cycle (CBB), Reverse Citrate cycle, 3-Hydroxypropionate bicycle (3HPB), Dicarboxylate-hydroxybutyrate cycle (DCHB), Hydroxypropionate Hydroxybutyrate cycle, and Reducive Acetyl-CoA pathway. Due to the complexity of reversible enzymatic reactions and the versatility of the involved enzymes, the Reductive Glycine pathway and reverse oxidative TCA cycle were not annotated in our analysis. We recovered 73,944 novel MAGs that, together with the other two MAG datasets, comprised the MarMAGs with 134,644 MAGs. The MarMAGs contain 31.2%(42047) high-quality and 68.78%(92617) medium-quality MAGs. Bacteria dominate the taxonomic composition of the MAGs at 89.89% (121046), and archaea at 10.11% (13618) spread across 135 phyla. Our analyses revealed 3.96% (5333) of the MAGs with genetic potential for at least one carbon fixation pathway, with CBB comprising 79.75% (4253), while 3HPB 0.02% (1) and DCHB 0.08% (4) have the least of them. Also, 28 MAGs affiliated to 5 phyla have the genetic potential for two pathways. Additionally, we are conducting phylogenetic analyses to explore the relatedness of MAGs based on their genetic capacities for carbon fixation and provide insights into the evolutionary adaptations of marine prokaryotes.
The MarMAGs database is a powerful tool for understanding marine prokaryotes' genetic potential. For example, investigating the genetic potential of carbon fixation within MarMAGs provided a detailed view of marine prokaryotes' diverse carbon fixation strategies. Our interactive web platform is a step forward in democratizing access to this valuable genome resource for researchers interested in microbial ecology, carbon cycling, and evolutionary biology in the marine environment.