Nitrate enrichment reveals a niche space for functionally and phylogenetically diverse populations of chemoautotrophs in salt marshes

Background/Question/Methods

: Carbon storage in salt marsh sediments depends, in part, on nutrient availability and metabolic activity of microbial organisms. Nitrate (NO3-) can facilitate heterotrophic microbial carbon decomposition by serving as an alternative electron acceptor in the absence of oxygen. Anthropogenic inputs of NO3- to coastal sediments could therefore increase respiration rates of the heterotrophic community resulting in decreased carbon storage potential. Alternatively, NO3- could be coupled with the oxidation of sulfur or other reduced compounds to fix inorganic carbon by stimulating chemoautotrophic activity, a process commonly referred to as dark carbon fixation (DCF). Microbial DCF is common within sublittoral and tidal sediments where it can support microbial assemblages through metabolic cross-feeding and removal of thermodynamic bottlenecks. We used shotgun metagenomic sequencing of sediment enriched with NO3- to identify the functional capacity for DCF under elevated NO3- concentrations. Three different sediment depths from multiple sites were examined in order to identify three characteristics of microbes with the capacity for DCF: 1) potential niche space, 2) phylogenetic diversity, and 3) functional potential of chemoautotrophs. We reconstructed draft genomes from the metagenomic data (MAGs) and used annotation tools, phylogenetic reconstruction and read mapping to address each of the characteristics respectively. Additionally, a pangenomic analysis of Sedimenticola and Chlorobium MAGs along with high quality reference genomes was conducted to identify common genomic features that may be important to DCF within salt marsh sediments.

Results/Conclusions

: We recovered a total of 113 MAGs and 59 of these contained the potential for DCF. Chemoautotrophs were detected in all NO3- enriched samples and at each of the three depths, indicative of a significant potential niche space. We recovered a phylogenetically diverse collection of organisms with the capacity for DCF and some are most closely related to reference genomes derived from chemoclines and oligotrophic habitats. MAGs with the capacity for DCF could be partitioned in to four distinct functional groups with unique features that may promote coexistence. Pangenomic analysis of Sedimenticola and Chlorobium revealed that central metabolic pathways, vitamin and cofactor metabolism are potentially important adaptations to inhabiting salt marsh sediments. These results suggest that the chemoautotrophic microbial community in salt marsh sediment contributes to carbon retention, especially when exposed to NO3 enrichment.