Metabolic exchange between Spartina alterniflora and sulfur chemosymbionts of the plant's root microbiome
EMSL Project ID
60422
Abstract
Vegetated coastal ecosystems are among the most intense carbon sinks in the biosphere, storing large amounts of carbon in their soils. Despite the fact that the root zone of coastal wetland plants is a hotspot for carbon and nutrient cycling, little is known about how plant-microbe interactions regulate coastal ecosystem function. This project characterizes the exchange of carbon and nitrogen that governs plant-microbe interactions across natural productivity gradients of Spartina alterniflora, the dominant plant species at the terrestrial-aquatic interface (TAI) on the U.S. Gulf of Mexico and Atlantic coasts. We have observed that sulfate-reducing and sulfur-oxidizing bacteria are overrepresented in the core root microbiome of S. alterniflora, with a high abundance of diazotrophic sulfur chemosymbionts. Our data suggest that S. alterniflora may obtain energy and/ or fixed nitrogen/carbon from sulfur oxidation in the root zone. However, the metabolic interactions responsible for coupling of the microbially-mediated sulfur cycle in the root zone to S. alterniflora primary productivity have not been studied. Given that nitrogen often limits productivity in coastal systems, we hypothesize that the mechanism fueling plant production is microbial sulfur oxidation coupled to diazotrophy in the same microorganism, bacteria from the Sedimenticolaceae family (e.g., Candidatus Thiodiazotropha). This research would represent the first experimental demonstration of energy conservation from symbiotic chemoautotrophy stimulating plant primary productivity. The core microbiome of Spartina will be investigated at sites spanning a latitudinal gradient along the U.S. Atlantic coast, leveraging collaborations with coastal TAI researchers from Massachusetts to Georgia(6 locations x 3 sites = 18 total samples per compartment), with our team or collaborators collecting paired soil and root samples for downstream analysis. A combination of shotgun metagenomics, metatranscriptomics, metaproteomics, metabolomics, and state-of-the-art biogeochemistry will be performed on samples. Thus far, we have sequenced shotgun metagenomic libraries from 24 Spartina root and soil samples(mean depth: 8.5 Gbp). Using our custom-designed bioinformatics pipeline, we binned 239 high-quality metagenome assembled genomes (MAGs; >50 Quality score), dereplicated to 160 genomospecies (< 95% ANI). We have successfully binned MAGs from putative sulfate-reducing and sulfur-oxidizing bacteria with high sequence identity to members of the Spartina core microbiome (Rolando et al., 2022), including sulfur chemosymbionts capable of nitrogen fixation (Candidatus Thiodiazotropha). In addition, we have used 15N incorporation to show that nitrogen fixation rates correlate with the abundance of sulfur-oxidizing bacteria in the Spartina root. We will map metatranscriptome and metaproteome libraries to binned MAGs in order to investigate the regulation of metabolic pathways in the plant holobiont. Plant and microbial metabolites will be characterized using FTICR and GC-mass spectrometry. Finally, in order to quantify the exchange of carbon and nitrogen between bacterial symbionts and the plant host, we propose to couple NanoSIMS with fluorescence in situ hybridization (FISH) using existing probes for sulfur chemosymbiotic bacteria on a subset of root samples(n = 10) incubated with a dual isotopic labeling approach (15N-N2 gas, and 13C-HCO3-). We will integrate multi-omics data to elucidate the plant-microbe-environment interactions that are critical for plant productivity to be sustained under environmental change.
Project Details
Project type
FICUS Research
Start Date
2022-10-01
End Date
N/A
Status
Active
Released Data Link
Team
Principal Investigator
Team Members