Abstract Detail

Symbioses: Plant, Animal, and Microbe Interactions

Peredo, Elena L [1], Pérez Castro, Sherlynette [1], Mason, Olivia [2], Vineis, Joe [3], Bowen, Jennifer [4], Mortazavi, Behzad [5], Ruff, Emil [1], Paul, Blair [1], Ganesh, Anakha [1], Giblin, Anne [1], Cardon, Zoe [1].

Uncultivated diversity of sulfur-cycling bacteria occurring in ecologically diverse vegetated salt marsh sediments.

Coastal salt marshes are dominated by a few extremely resilient plant taxa adapted to the halophytic and anoxic conditions of a tidal system. In addition to physiological adaptations, these marsh plant species rely on the symbiotic relationships established with the microorganisms inhabiting the rhizosphere to survive the extreme conditions in tidal areas. Sulfur-cycling bacteria comprise a large fraction of the microbial community in roots playing an essential role as a recycling and detoxification system. Sulfate reducing bacteria (SRB) thrive on the carbon compounds lost from living roots and produce sulfide that is toxic to the plants. Sulfur oxidizing bacteria (SOX) transform that sulfide back into nontoxic sulfate that can be absorbed by the plants, contributing to the overall productivity of the ecosystem. As human actions and acceleration of sea level rise threaten the health of salt marshes, understanding the symbiotic relationships between plants and sulfur-cycling bacteria is essential to better develop strategies aiming to preserve the health of these coastal systems. Understanding the diversity and specific genomic of plant-associated bacteria characteristics can provide key insight to the mechanisms controlling this symbiotic partnership. However, the technical difficulties of assembling metagenome-assembled genomes (MAGs) in such a diverse environment as the sediments in salt marshes has had the consequence of sulfur-cycling bacteria being underrepresented in reference metagenomic databases. To fill that gap, implemented an open-source standardized bioinformatic pipeline to assemble (MEGAHIT), bin (metaWRAP), functionally-annotate (DRAM), and compare (GTDB-Tk, Anvi’o, PATRIC) metagenomes using publicly available, deeply sequenced datasets from sediments nearby roots of Sporobolus alterniflorus, S. pumilus, Juncus roemerianus sampled in marshes in Alabama and Massachusetts. We use a comparative metagenomic approach in ecologically diverse salt marsh environments to infer shared patterns among microbial genes, organisms, and communities across contrasting latitudes and dominant vegetation. We reconstructed 118 medium-high quality MAGs (≥90% complete with ≤5% contamination) and identified 38 MAGs encoding full sulfur oxidation and/or sulfate reduction pathways. All of them belonged to uncultured lineages. SRB MAGs were mostly from Alabama and identified as Acidobacteria, Bacteroidota, Gemmatimonadota, and Desulfobacterota. SOX MAGs fell within Proteobacteria and were assembled from each site and plant species. We demonstrate segregation by site and host of the metagenomic communities using a mapping-based approach and NMDS analysis. We selected eight MAGs to further explore the site-specific genomic diversity within the identified SOX and SRB MAGs. First, we use Anvi’o profiling to identify the potential sample-specific variability by analyzing the average entropy of selected genes. Secondly, we use a reference-guided reassembly strategy to produce sample-specific metagenomes combined with Anvi’o pangenomic workflow to identify site and host specific gene clusters among the reconstructed MAGs. Finally, we identify the presence of diversity-generating retroelements (DGRs) in the genomes of two of sulfur-oxidizing bacteria. In sum, with our work we reveal an under-explored reservoir of novel lineages, genomic diversity, and metabolic potentials within the microbial communities inhabiting ecologically diverse salt marsh environments. Most interestingly, although we identified taxonomic groups expected from previous salt marsh work, we observed noticeable site and host specific genomic variation.

1 - Marine Biological Laboratory (USA), 7 MBL st, Woods Hole, Massachusetts, 02543, United States
2 - Florida State University, Earth, Ocean and Atmospheric Science, Tallahassee, FL, 32306 , USA
3 - Princeton University, Department of Geosciences, USA
4 - Northeastern University, Marine and Environmental Sciences, MA, USA
5 - University of Alabama, Biological Sciences, AL, USA

Keywords:
Symbiosis
Metagenomics
Gene diversity
Comparative -omics.

Presentation Type: Oral Paper
Number: SYM2006
Abstract ID:104
Candidate for Awards:None