Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29991752", "kind": "science-record", "revision": 4, "content_hash": "sha256:693c2ce82ef08395f87d6771dbd6d44d50aea89331e51504164b55527b1935c7", "created_at": "2026-11-01T15:40:35Z", "updated_at": "2026-11-01T21:21:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits.", "doi": "10.1038/s41598-018-28613-5", "pmid": "29991752", "authors": ["Yuchen Han", "Giorgio Gonnella", "Nicole Adam", "Axel Schippers", "Lia Burkhardt", "Stefan Kurtz", "Ulrich Schwarz-Schampera", "Henrike Franke", "Mirjam Perner"], "journal": "Scientific reports", "year": 2018, "abstract": "To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and the Pelagia vent fields along the Indian Ridge. In total 19.8 million 16S rRNA tags from 14 different sites were analyzed and the microbial communities were compared with each other and with publicly available data sets from other marine environments. The chimneys appear to provide habitats for microorganisms that are not found or only detectable in very low numbers in other marine habitats. The chimneys also host rare organisms and may function as a vital part of the ocean's seed bank. Many of the reads from active and inactive chimney samples were clustered into OTUs, with low or no resemblance to known species. Since we are unaware of the chemical reactions catalyzed by these unknown organisms, the impact of this diversity loss and bio-geo-coupling is hard to predict. Given that chimney structures can be considered SMS analogues, removal of sulfide deposits from the seafloor in the Kairei and Pelagia fields will most likely alter microbial compositions and affect element cycling in the benthic regions and probably beyond.", "claims": [{"id": "claim-method", "statement": "The UPGMA clustering of the samples, based on beta diversity analyses, yielded quite different results depending on whether de novo and/or reference-based OTUs were considered and whether the Sørensen-Dice or Bray-Curtis index was used for analyses (Fig. 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29991752", "locator": "sections[9] \"Specificity and relatedness of the different Kairei and Pelagia communities\" paragraph 2", "quote": "The UPGMA clustering of the samples, based on beta diversity analyses, yielded quite different results depending on whether de novo and/or reference-based OTUs were considered and whether the Sørensen-Dice or Bray-Curtis index was used for analyses (Fig. 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Sequence data have been deposited in the National Center for Biotechnology Information Sequence Read Archive (SRA) under accession no. SRP120106.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29991752", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "Sequence data have been deposited in the National Center for Biotechnology Information Sequence Read Archive (SRA) under accession no. SRP120106."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using beta-diversity analyses of 19.8 million 16S rRNA tags from 14 sites, compared with publicly available marine datasets, the study found that hydrothermal chimneys host habitat-specific microorganisms and that their removal by SMS mining would most likely alter microbial compositions and affect element cycling.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29991752", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total 19.8 million 16S rRNA tags from 14 different sites were analyzed and the microbial communities were compared with each other and with publicly available data sets from other marine environments."}, {"asset": "source:pmid:29991752", "locator": "sections[2] \"Results and Discussion\" paragraph 2", "quote": "Using beta diversity analyses we investigated the similarities and dissimilarities among the samples in the Kairei and Pelagia environments and illustrated their relation to samples from comparable biotopes available from the literature."}, {"asset": "source:pmid:29991752", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Given that chimney structures can be considered SMS analogues, removal of sulfide deposits from the seafloor in the Kairei and Pelagia fields will most likely alter microbial compositions and affect element cycling in the benthic regions and probably beyond."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using beta-diversity analyses of 19.8 million 16S rRNA tags from 14 sites, compared with publicly available marine datasets, the study found that hydrothermal chimneys host habitat-specific microorganisms and that their removal by SMS mining would most likely alter microbial compositions and affect element cycling.", "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:29991752"], "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": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. 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