Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes

Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.