Soybean Leaf Proteomic Profile Influenced by Rhizobacteria Under Optimal and Salt Stress Conditions.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35401626", "kind": "science-record", "revision": 4, "content_hash": "sha256:63abdb4e3cecbf0f5a5b9b3f661ab2325e177df4b12e843b18138b4b401e73af", "created_at": "2026-11-01T18:14:13Z", "updated_at": "2026-11-01T22:06:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Soybean Leaf Proteomic Profile Influenced by Rhizobacteria Under Optimal and Salt Stress Conditions.", "doi": "10.3389/fpls.2022.809906", "pmid": "35401626", "authors": ["Gayathri Ilangumaran", "Sowmyalakshmi Subramanian", "Donald L Smith"], "journal": "Frontiers in plant science", "year": 2022, "abstract": "Soil salinity is a major abiotic stressor inhibiting plant growth and development by affecting a range of physiological processes. Plant growth promoting rhizobacteria (PGPR) are considered a sustainable option for alleviation of stress and enhancement of plant growth, yet their mode of action is complex and largely unexplored. In this study, an untargeted proteomic approach provided insights into growth and stress response mechanisms elicited in soybean plants by Rhizobium sp. SL42 and Hydrogenophaga sp. SL48 and co-inoculated with Bradyrhizobium japonicum 532C. The plants were grown under optimal and salt-stressed conditions up to their mid-vegetative stage; shoot growth variables were increased in the bacteria-treated plants. Shotgun proteomics of soybean leaf tissue revealed that a number of proteins related to plant growth and stress tolerance were modulated in the bacterial inoculation treatments. Several key proteins involved in major metabolic pathways of photosynthesis, respiration, and photorespiration were upregulated. These include photosystem I psaK, Rubisco subunits, glyceraldehyde-3-phosphate dehydrogenase, succinate dehydrogenase, and glycine decarboxylase. Similarly, stress response proteins such as catalase and glutathione S-transferase (antioxidants), proline-rich precursor protein (osmolyte), and NADP-dependent malic enzyme (linked to ABA signaling) were increased under salt stress. The functions of proteins related to plant growth and stress adaptation led to an expanded understanding of plant-microbe interactions. These findings suggest that the PGPR strains regulated proteome expression in soybean leaves through multiple signaling pathways, thereby inducing salinity tolerance, and improving plant growth in the presence of this abiotic stress challenge. Data are available via ProteomeXchange with identifier PXD025596.", "claims": [{"id": "claim-method", "statement": "The data were analyzed using the SAS statistical package v.9.4 (SAS Institute Inc., Cary, NC, United States) with Proc Mixed model at a 95% confidence interval and multiple means comparison was by Tukey’s HSD (honest significant difference) at α = 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35401626", "locator": "sections[9] \"Statistical Analysis\" paragraph 2", "quote": "The data were analyzed using the SAS statistical package v.9.4 (SAS Institute Inc., Cary, NC, United States) with Proc Mixed model at a 95% confidence interval and multiple means comparison was by Tukey’s HSD (honest significant difference) at α = 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are publicly available. This data can be found here: Data are available via ProteomeXchange with identifier PXD025596.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35401626", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are publicly available. This data can be found here: Data are available via ProteomeXchange with identifier PXD025596."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:35401626"], "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:PXD025596"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:regression_modelling_mixed_effects", "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:PXD025596"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:regression_modelling_mixed_effects"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35401626", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpls.2022.809906", "sha256": "sha256:1eec50b680fc694c94b817b931ed64a4bcec0d0c496938068c0cf1c841820d9e", "bytes": 59584, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpls.2022.809906", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8987779", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD025596", "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=PXD025596", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD025596", "version": null, "note": "The original contributions presented in the study are publicly available. This data can be found here: Data are available via ProteomeXchange with identifier PXD025596.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are publicly available. This data can be found here: Data are available via ProteomeXchange with identifier PXD025596.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Soybean leaf proteomic profile influenced by rhizobacteria under optimal and salt stress conditions", "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD025596 not downloaded", "asset:data:geo:PXD025596 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "mixed_effects", "label": "Regression modelling", "dsl_operations": [], "missing_operations": ["regression_modelling_mixed_effects"], "expressible": false, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The data were analyzed using the SAS statistical package v.9.4 (SAS Institute Inc., Cary, NC, United States) with Proc Mixed model at a 95% confidence interval and multiple means comparison was by Tukey’s HSD (honest significant difference) at α = 0.05."}}], "targets": [], "gaps": ["method.regression_modelling_mixed_effects"]}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["regression_modelling_mixed_effects"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mixed_effects."}, "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": ["PXD025596", "PXD025596 and 10.6019/PXD025596"], "resolved_accessions": ["PXD025596"], "statements": ["The original contributions presented in the study are publicly available. This data can be found here: Data are available via ProteomeXchange with identifier PXD025596."], "basis": "The paper names PXD025596 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35401626", "data:geo:PXD025596"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "regression_modelling_mixed_effects", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD025596"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:41:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16223, "completion_tokens": 1424, "cached_tokens": 128}}, "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:35401626", "type": "paper", "label": "pmid:35401626"}, {"id": "source:pmid:35401626", "type": "manuscript", "label": "PMID 35401626 full text"}, {"id": "data:geo:PXD025596", "type": "dataset", "label": "GEO PXD025596"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35401626", "type": "paper", "label": "pmid:35401626"}, {"id": "source:pmid:35401626", "type": "manuscript", "label": "PMID 35401626 full text"}, {"id": "data:geo:PXD025596", "type": "dataset", "label": "GEO PXD025596"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35401626", "type": "extraction", "used": ["source:pmid:35401626"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD025596", "type": "accession_resolution", "used": ["data:geo:PXD025596"], "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:35401626", "parent_hash": "sha256:2b122def7ca9a124c1b45c4f0a14961e9df564cd4fa79113dd1c454405dc1f56", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD025596 licence not read", "asset:data:geo:PXD025596 not downloaded", "execution.not_run", "method.regression_modelling_mixed_effects", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:regression_modelling_mixed_effects"], "assays": [{"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The data were analyzed using the SAS statistical package v.9.4 (SAS Institute Inc., Cary, NC, United States) with Proc Mixed model at a 95% confidence interval and multiple means comparison was by Tukey’s HSD (honest significant difference) at α = 0.05."], "order_basis": "analysis_only", "id": "assay:1"}]}