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Abstract Detail

Symbioses: Plant, Animal, and Microbe Interactions

Peredo, Elena [1], Pérez Castro, Sherlynette [2], Mason, Olivia [3], Vineis, Joseph [4], Bowen, Jennifer [4], Mortazavi, Behzad [5], Ruff, S. Emil [6], Paul, Blair [7], Anakha, Ganesh [7], Giblin, Anne E. [7], Cardon, Zoe G. [6].

Genomic diversity of uncultured sulfur cycling bacterial communities isolated from rhizosphere sediments in Massachusetts and Alabama salt marshes.

Coastal salt marshes are dominated by only a few extremely resilient plant taxa. These marsh plant species rely on a rhizosphere microbiome to act as a recycling and detoxification system. Though toxic sulfide is produced by abundant sulfate reducing bacteria (SRB) that thrive on the carbon compounds lost from living roots, sulfur oxidizing bacteria (SOX) can transform that sulfide back into nontoxic sulfate. The diversity of salt marsh sulfur cycling bacteria is therefore of great interest for salt marsh health, but these bacteria are underrepresented in reference metagenomic databases. To fill that gap, we capitalized on available deep shotgun sequencing from multiple research groups to coalesce datasets from ecologically diverse salt marsh environments, enabling investigation of commonalities and differences among microbial genes, organisms, and communities across contrasting latitudes and dominant vegetation.
We designed and 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 under smooth cordgrass (Sporobolus alterniflorus), saltmeadow cordgrass (Sporobolus pumilus), and black needlerush (Juncus roemerianus), sampled in marshes in Alabama and Massachusetts.  
Assembly and binning with stringent criteria (≥ 90% complete with ≤ 5% contamination)   resulted in the reconstruction of 40 bacterial metagenome-assembled genomes (MAGs) containing genes encoding full sulfur oxidation and/or sulfate reduction pathways. All of these MAGs belonged to uncultured lineages. SOX MAGs were assembled from each site and plant species, and they fell within Proteobacteria. SRB MAGs were mostly from Alabama and identified as Acidobacteria, Bacteroidota, Gemmatimonadota, and Desulfobacterota. Six SOX and three SRB MAGs were affiliated with the Uncultivated Bacteria and Archaea (UBA). A  mapping-based approach and NMDS analysis demonstrates that the microbial communities represented by the MAGs in the 25 samples segregate by site  and by vegetation. Finally, we explored the genomic diversity within the identified SOX and SRB MAGs across sites. We used a reference-guided reassembly strategy (metaWRAP) to produce sample-specific metagenome reassembled genomes (MRAGs), and   used Anvi'o pangenomic workflow to annotate each MRAG, identify shared and site/host specific gene clusters, and calculate comparative whole-genome similarity metrics such as Average Nucleotide Identity (ANI).  
In sum, our robust analytical pipelines, designed to distill MAGs from diverse datasets, revealed an underexplored reservoir of novel lineages and metabolic potentials within the microbial communities inhabiting ecologically diverse salt marsh environments. Most interestingly, although were identified taxonomic groups expected from previous salt marsh work, we observed notable site and host specific genomic variation.

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1 - Marine Biological Laboratory, The Ecosystems Center, 7 MBL St, Starr Building, Woods Hole, MA, 02543, United States
2 - Marine Biological Laboratory, The Ecosystems Center, 7 Mbl St, Woods Hole, MA, 02543, United States
3 - Florida State University, EOAS, 1011 Academic Way, Tallahassee, FL, 32304 , USA
4 - Northeastern University, Marine Science Center, Nahant, MA, 01908, USA
5 - The University of Alabama, Department of Biological Sciences, SEC 1325, Tuscaloosa, AL, 35487, USA
6 - Marine Biological Laboratory, The Ecosystems Center, 7 Mbl St, Woods Hole, MA, 02543, USA
7 - Marine Biological Laboratory, 7 Mbl St, Woods Hole, MA, 02543, USA


Presentation Type: Oral Paper
Session: SYMB1, Symbioses: Plant, Animal and Microbe Interactions 1
Location: /
Date: Monday, July 19th, 2021
Time: 1:15 PM(EDT)
Number: SYMB1004
Abstract ID:760
Candidate for Awards:None

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