Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36226293", "kind": "science-record", "revision": 3, "content_hash": "sha256:ecc3462d00c03dae2f0cd8e1b79987b1c65bef56190f6a98e73b39e6903a499f", "created_at": "2026-11-01T18:15:35Z", "updated_at": "2026-11-01T21:29:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches.", "doi": "10.3389/fpls.2022.988709", "pmid": "36226293", "authors": ["Marion Schilling", "Alessandra Maia-Grondard", "Raymonde Baltenweck", "Emilie Robert", "Philippe Hugueney", "Christophe Bertsch", "Sibylle Farine", "Eric Gelhaye"], "journal": "Frontiers in plant science", "year": 2022, "abstract": "Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called \"amadou,\" one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites (extractives) and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern was demonstrated, and proteomic analysis identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species, and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche. Proteomics data are available via ProteomeXchange with identifier PXD036889.", "claims": [{"id": "claim-method", "statement": "Shapiro–Wilk test was used for data normality check when relevant. Kruskal-Wallis tests with Conover-Iman multiple comparisons test were used for nonparametric tests and Student Newman–Keuls (SNK-test) for parametric tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36226293", "locator": "sections[13] \"Statistical analyses\" paragraph 2", "quote": "Shapiro–Wilk test was used for data normality check when relevant. Kruskal-Wallis tests with Conover-Iman multiple comparisons test were used for nonparametric tests and Student Newman–Keuls (SNK-test) for parametric tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifier PXD036889.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36226293", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifier PXD036889."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Fomitiporia mediterranea degraded grapevine sawdust more efficiently than beech sawdust, showed no significant degradation of spruce, and produced relatively more oxidoreductases involved in lignin and extractive degradation on grapevine cultures.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36226293", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture."}, {"asset": "source:pmid:36226293", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Moreover, on both substrates, a simultaneous degradation pattern was demonstrated, and proteomic analysis identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Fomitiporia mediterranea degraded grapevine sawdust more efficiently than beech sawdust, showed no significant degradation of spruce, and produced relatively more oxidoreductases involved in lignin and extractive degradation on grapevine cultures.", "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:36226293"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD036889"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD036889"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36226293", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpls.2022.988709", "sha256": "sha256:483b0e41c34b1f4ef1ca6a6e53d51008b8a40774df33b2483da658e2ee7ef5bb", "bytes": 84391, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpls.2022.988709", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9549746", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD036889", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD036889", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD036889", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifier PXD036889.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifier PXD036889.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Wood degradation by Fomitiporia mediterranea M. Fischer: physiologic, metabolomic and proteomic approaches", "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD036889 not downloaded", "asset:data:geo:PXD036889 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Tukey test, Student Newman–Keuls test, Kruskal-Wallis test with Conover-Iman multiple comparisons test, and Shapiro–Wilk test for normality", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Shapiro–Wilk test was used for data normality check when relevant. Kruskal-Wallis tests with Conover-Iman multiple comparisons test were used for nonparametric tests and Student Newman–Keuls (SNK-test) for parametric tests."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Tukey test, Student Newman–Keuls test, Kruskal-Wallis test with Conover-Iman multiple comparisons test, and Shapiro–Wilk test for normality), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD036889"], "resolved_accessions": ["PXD036889"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifier PXD036889."], "basis": "The paper names PXD036889 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36226293", "data:geo:PXD036889"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD036889"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:10:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 23978, "completion_tokens": 1452, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36226293", "type": "paper", "label": "pmid:36226293"}, {"id": "source:pmid:36226293", "type": "manuscript", "label": "PMID 36226293 full text"}, {"id": "data:geo:PXD036889", "type": "dataset", "label": "GEO PXD036889"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36226293", "type": "paper", "label": "pmid:36226293"}, {"id": "source:pmid:36226293", "type": "manuscript", "label": "PMID 36226293 full text"}, {"id": "data:geo:PXD036889", "type": "dataset", "label": "GEO PXD036889"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36226293", "type": "extraction", "used": ["source:pmid:36226293"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD036889", "type": "accession_resolution", "used": ["data:geo:PXD036889"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36226293", "parent_hash": "sha256:d4b14d43df1844b599647edea04fe74b3aed74829494c8efe3a5f049ba68f098", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD036889 licence not read", "asset:data:geo:PXD036889 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}