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Marine Microbiology Initiative - Gordon and Betty Moore Foundation

Comparative ‘omics’ of deep-sea Bathymodiolus symbionts

Bathymodiolus mussels are among the most abundant animals at hydrothermal vents and cold seeps worldwide. They can form vast and dense communities in these habitats because symbiotic bacteria provide them with a source of nutrition. We are currently sequencing the genomes of these chemosynthetic symbionts from diverse Bathymodiolus species from hydrothermal vents and cold seeps around the world. The goals of this project are i) to gain a better understanding of metabolic pathways for energy and carbon acquisition, as well as for the uptake and use of nutrients in chemosynthetic symbionts, and ii) identify common metabolic pathways in chemosynthetic symbionts and their closest free-living relatives, and (iii) to identify metabolic pathways that are specific to some symbiont strains.

The status of our large-scale metagenome sequencing project can be seen in the table below. For some species we also have corresponding transcriptome or proteome data.

The following data have been published in the following studies:

Sayavedra L, Ansorge R, Rubin-Blum M, Leisch N, Dubilier N, Petersen JM. Horizontal acquisition, followed by expansion and diversification, of toxin-related genes in deep-sea mussels and sponges. In review at eLife.

Rubin-Blum M, Antony CP, Borowski C, Sayavedra L, Pape T, Sahling H, Bohrmann G, Redmond MC, Valentine DL, Dubilier N (2017) Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps. Nature Microbiology, 2: doi:10.1038/nmicrobiol.2017.93

Assie A, Borowski C, van der Heijden K, Raggi L, Geier B, Leisch N, Schimak MP, Dubilier N, Petersen JP (2016) A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria. Environ. Microbiol. Reports. doi:10.1111/1758-2229.12442

Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, and Dubilier N (2011) Hydrogen is an energy source for hydrothermal vent symbioses. Nature 476: 176–180.

Ponnudurai RP, Kleiner M, Sayavedra L, Petersen J, Moche M, Otto A, Becher D, Takeuchi T, Satoh N, Dubilier N, Schweder T, Markert S (2017) Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis. ISME Journal, 2: 463-477.

Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Shoguchi E, Satoh N, Reusch TBH, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM (2015) Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 4:e07966,1-39. doi:10.7554/eLife.07966



Published data
Year published Dataset title Dataset ID and/or URL
2011, 2015 Endosymbiont of Bathymodiolus sp. PRJNA65421
2015 Genome of sulfur oxidizer endosymbiont of Bathymodiolus azoricus from Menez Gwen (BazSymA) PRJEB8263
2015 Genome of sulfur oxidizer endosymbiont of Bathymodiolus azoricus from Menez Gwen (BazSymB) PRJEB8264
2015 Mitochondrial COI gene for cytochrome oxidase subunit 1 LN833433 - LN833440
2015 Transcriptome of sulfur oxidizer endosymbiont of Bathymodiolus azoricus PRJEB7941
2015 Transcriptome of sulfur oxidizer endosymbiont of Bathymodiolus sp. 9° South PRJEB7943
2015 Bathymodiolus azoricus thioautotrophic gill symbiont partial 16S rRNA gene, isolate BazSymB LN871183
2016  Methanotrophic symbionts of Bathymodiolus azoricus and of Bathymodiolus sp. PRJEB13769 and PRJEB13047
2016  Proteomics dataset of Bathymodiolus azoricus from Menez Gwen PXD004061
2017 Proteomics of Cycloclasticus endosymbiont of deep-sea mussel Bathymodiolus heckerae from Campeche Knolls, southern Gulf of Mexico PXD005351



This table lists sequencing data that we are in the process of analyzing and are therefore not yet included in any published study. Several draft genomes were uploaded to and can be accessed via the Integrated Microbial Genomes (IMG) database of the DOE Joint Genome Institute (http://img.jgi.doe.gov/); a list with the corresponding project IDs has also been uploaded to Zenodo (https://zenodo.org/record/160958#.WAJmvjL5yCY and https://zenodo.org/record/999554#.Wc6Pktxx2po). The remaining draft genomes are in the process of submission to NCBI. If you are interested in these datasets, please let us know.

 
Sampling locationNo. of inds.SOX*MOX**Other symbiontsNo. of transcriptomesNo. of proteomes
South MAR Lilliput3116
South MAR Clueless51 (IMG: Ga0076941)1
South MAR Wideawake11
Logatchev711Ca. Endonucleobacter6
Semenov33 (IMG: Ga0101657- Ga0101659)1 (IMG: Ga0076937)3
Menez Gwen55 (IMG: Ga0101651- Ga0101655)Epsilon32 ***
Lucky Strike2016 (IMG: Ga0073391, Ga0101676- Ga0101691)2 (IMG: Ga0073390; Ga0076935)5 (acc. no.
PRJEB12674)
Rainbow55 (IMG: Ga0101630- Ga0101634)3
East Pacific Rise, Crab Spa33 (IMG: Ga0101625- Ga0101627)
Gulf of Mexico, Chapopote521Cycoclasticus
Gulf of Mexico, GC600211 (IMG: Ga0076939)Epsilon
Gulf of Mexico, MC64011Ca. Endonucleobacter, Epsilon3
Gulf of Mexico, GC24911 (IMG: Ga0076933)
* SOX = Sulfur oxidizing symbiont
** MOX = Methane oxidizing symbiont
*** Published in Ponnudurai et al. (in press, see above)

Comparative 'omics' of gutless oligochaetes

Gutless oligochaetes were found to associate with a wide variety of beneficial, microbial symbionts. We are using multi-'omic' approaches to reveal the functions of the different symbionts in the symbiosis and to identify how the association with symbionts from different phylogenetic clades may have shaped the evolution of the hosts. 

The sequencing data we obtained is in the process of analyzing and therefore not yet included in any published study. Several draft genomes were uploaded to an can be accessed via the Integrated Microbial Genomes (IMG) database of the DOE Joint Genome Institute (http://img.jgi.doe.gov/); a list with the corresponding project IDs has also been uploaded to Zenodo (https://zenodo.org/record/998566#.Wc6Nz9xx2po).The remaining draft genomes are in the process of submission to NCBI. If you are interested in these datasets, please let us know. 

Protocols for mass spectrometry imaging

We uploaded MS-imaging datasets from different animals (Bathymodiolus spp., Kentrophoros sp., Lumbricus terrestris, Olavius algarvensis, Paracatenula sp.) and plants (Posidonia oceanica) to the open access servers Metaspace (http://annotate.metaspace2020.eu/#/datasets) and Proteome Exchange (http://Proteomexchange.org/). A list with the corresponding project IDs and metadata of the samples has been uploaded to Zenodo

2016:

(https://zenodo.org/record/160973#.WAJoKzL5yCY).

2017:

(https://zenodo.org/record/998574#.Wc6NQdxx2po)


Link to files:

Micro-computed tomography of the host-microbe complex

Host-microbe symbioses are complexly organized, multi-organism assemblies embedded into the anatomic frame of the host organism. Understanding how the bacteria are distributed in specialized host organs and which metabolites are present will give us clues on metabolic activity, colonization patterns and micro environments. We aim to visualize the 3D micro-anatomy of the host to quantify the biomass of the associated microbes.

Therefore, we are optimizing the application of high-resolution tomographic techniques such as phase contrast synchrotron micro computed tomography (PC SRµCT) to image the undisturbed 3D microanatomy of the mussel gills and symbiont-containing host cells.

 

Whole animal micro-CT scans of:

Bathymodiolus childressi:

https://figshare.com/s/4a44acd3208bb44364f0

Bathymodiolus azoricus:

https://figshare.com/s/01ab2ae97457cf2631bf

 

Video of multimodal project (µCT-MALDI-MSI-FISH):

https://figshare.com/s/520c77cc37bff2cc1d93

 

Links to online protocols:

https://www.protocols.io/view/seagrass-metabolite-extraction-for-gc-ms-based-met-ju7cnzn

https://www.protocols.io/private/6ba62d5de41ddfca9e885420e9e41975

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