Mixotrophic Growth Under Micro-Oxic Conditions in the Purple Sulfur Bacterium "Thiodictyon syntrophicum".

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It has been found that the purple sulfur bacterium \"Thiodictyon syntrophicum\" strain Cad16T, belonging to the Chromatiaceae, fixes around 26% of all bulk inorganic carbon in the chemocline, both during day and night. With this study, we elucidated for the first time the mode of carbon fixation of str. Cad16T under micro-oxic conditions with a combination of long-term monitoring of key physicochemical parameters with CTD, 14C-incorporation experiments and quantitative proteomics using in-situ dialysis bag incubations of str. Cad16T cultures. Regular vertical CTD profiling during the study period in summer 2017 revealed that the chemocline sank from 12 to 14 m which was accompanied by a bloom of cyanobacteria and the subsequent oxygenation of the deeper water column. Sampling was performed both day and night. CO2 assimilation rates were higher during the light period compared to those in the dark, both in the chemocline population and in the incubated cultures. The relative change in the proteome between day and night (663 quantified proteins) comprised only 1% of all proteins encoded in str. Cad16T. Oxidative respiration pathways were upregulated at light, whereas stress-related mechanisms prevailed during the night. These results indicate that low light availability and the co-occurring oxygenation of the chemocline induced mixotrophic growth in str. Cad16T. Our study thereby helps to further understand the consequences micro-oxic conditions for phototrophic sulfur oxidizing bacteria. The complete proteome data have been deposited to the ProteomeXchange database with identifier PXD010641.", "claims": [{"id": "claim-method", "statement": "Raw data was statistically analyzed using t-tests in Excel (Microsoft Office 2010, v-0.14.0.7168.5000).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30891015", "locator": "sections[7] \"14C-Incubations\" paragraph 3", "quote": "Raw data was statistically analyzed using t-tests in Excel (Microsoft Office 2010, v-0.14.0.7168.5000)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Genomic Data Availability\nThe complete genome of str. Cad16T (Luedin et al., 2018a) is available under the GenBank assembly GCA_002813775.1.\nProteomic Data Availability\nThe complete proteomic data of str. Cad16T have been deposited to the ProteomeXchange Consortium (ProteomeXchange Datasets2) via the PRIDE partner repository (Vizcaíno et al., 2012) under the accession PXD010641 and project DOI 10.6019/PXD010641.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30891015", "locator": "sections[12] \"Genomic Data Availability\" paragraphs 1-2", "quote": "Genomic Data Availability\nThe complete genome of str."}, {"asset": "source:pmid:30891015", "locator": "sections[12] \"Genomic Data Availability\" paragraph 2", "quote": "Cad16T (Luedin et al., 2018a) is available under the GenBank assembly GCA_002813775.1."}, {"asset": "source:pmid:30891015", "locator": "sections[13] \"Proteomic Data Availability\" paragraphs 1-2", "quote": "Proteomic Data Availability\nThe complete proteomic data of str."}, {"asset": "source:pmid:30891015", "locator": "sections[13] \"Proteomic Data Availability\" paragraph 2", "quote": "Cad16T have been deposited to the ProteomeXchange Consortium (ProteomeXchange Datasets2) via the PRIDE partner repository (Vizcaíno et al., 2012) under the accession PXD010641 and project DOI 10.6019/PXD010641."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30891015"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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