Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem

• Published in: Microbiome Vol. 10; no. 1; pp. 1 - 126
• Main Authors: Broman, Elias, Izabel-Shen, Dandan, Rodríguez-Gijón, Alejandro, Bonaglia, Stefano, Garcia, Sarahi L., Nascimento, Francisco J. A.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 15-08-2022; BMC
• Subjects: Bacteria; Benthic; Bioinformatics and Systems Biology; Bioinformatik och systembiologi; Carbon; Climate change; DNA; Ecology; Ekologi; Genes; Genomes; Geochemistry; Geokemi; Metabolic pathways; Metabolism; Metagenomics; Microbial; Microbiology; Microorganisms; Mikrobiologi; Nitrogen; Nutrient transport; Ocean floor; Oceanografi, hydrologi, vattenresurser; Oceanography, Hydrology, Water Resources; Oxygen; Oxygenation; Resource availability; Salinity; Salinity effects; Sediments; Software; Stoichiometry; Baltic Sea
• ISSN: 2049-2618; 2049-2618
• DOI: 10.1186/s40168-022-01321-z

Background Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. Results The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. Conclusions This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract