{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T06:52:45Z","timestamp":1791010365988,"version":"4.1.0"},"reference-count":54,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["212266"],"award-info":[{"award-number":["212266"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["197391"],"award-info":[{"award-number":["197391"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Environmental Microbiology"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Auxotrophy, the inability of bacteria to synthesize one or multiple essential metabolites, is thought to be common among bacteria. However, studies often rely on either bioinformatic genome\u2010based prediction of auxotrophies or on experiments with low strain numbers. Here, we combine experimental and bioinformatic approaches to assess amino acid auxotrophies among 315 co\u2010isolated natural\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    strains from pond and soil habitats. Experiments revealed that\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    isolates are predominantly prototrophs. We identified one histidine auxotroph, one auxotroph with complex intertwined dependencies and four \u2018fragile\u2019 phenotypes showing delayed growth without supplemented amino acids. Applying three bioinformatic pipelines largely confirmed experimental data but yielded specific biases in auxotrophy over\u2010 or underestimation. Moreover, none of the pipelines could resolve the genetic basis of the slow\u2010growing phenotypes or of more complex dependencies. Our analysis further revealed the existence of multiple alternative biosynthesis pathways for methionine, proline and phenylalanine, with significant pathway enrichments being linked to phylogeny and habitat. We conclude that combining experiments with bioinformatics is a powerful approach to assess the metabolic potential of environmental bacteria. Moreover, taxa like\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    can be predominantly prototrophic possibly owing to their generalist lifestyle, thus calling for nuanced ecological concepts predicting auxotrophy levels based on lifestyle and habitat.\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.70434","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T06:05:04Z","timestamp":1791007504000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Low Levels of Amino Acid Auxotrophy Among Environmental\n                    <i>Pseudomonas<\/i>\n                    Isolates"],"prefix":"10.1111","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-9802-647X","authenticated-orcid":false,"given":"Simon","family":"Mar\u00e9chal","sequence":"first","affiliation":[{"name":"Department of Quantitative Biomedicine University of Zurich  Zurich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4145-277X","authenticated-orcid":false,"given":"Benjamin","family":"Heiniger","sequence":"additional","affiliation":[{"name":"Method Development and Analytics Agroscope  Zurich Switzerland"},{"name":"PhD Program Systems Biology Zurich Life Sciences Graduate School  Zurich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3071-5747","authenticated-orcid":false,"given":"Shaohua","family":"Gu","sequence":"additional","affiliation":[{"name":"College of Resources and Environmental Sciences, State Key Laboratory of Nutrient Use and Management (SKL\u2010NUM), National Academy of Agriculture Green Development, China Agricultural University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7408-9866","authenticated-orcid":false,"given":"Swagatika","family":"Dash","sequence":"additional","affiliation":[{"name":"Department of Ecology, School of Biology\/Chemistry University of Osnabr\u00fcck  Osnabr\u00fcck Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8148-7257","authenticated-orcid":false,"given":"Christian H.","family":"Ahrens","sequence":"additional","affiliation":[{"name":"Method Development and Analytics Agroscope  Zurich Switzerland"},{"name":"Swiss Institute of Bioinformatics  Zurich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4084-6679","authenticated-orcid":false,"given":"Rolf","family":"K\u00fcmmerli","sequence":"additional","affiliation":[{"name":"Department of Quantitative Biomedicine University of Zurich  Zurich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,2]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"2006.0008","DOI":"10.1038\/msb4100050","article-title":"Construction of \n                     Escherichia coli\n                   K\u201012 In\u2010Frame, Single\u2010Gene Knockout Mutants: The Keio Collection","volume":"2","author":"Baba T.","year":"2006","journal-title":"Molecular Systems Biology"},{"key":"e_1_2_10_3_1","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/s41467-017-00509-4","article-title":"Siderophore Cheating and Cheating Resistance Shape Competition for Iron in Soil and Freshwater Pseudomonas Communities","volume":"8","author":"Butait\u0117 E.","year":"2017","journal-title":"Nature Communications"},{"key":"e_1_2_10_4_1","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1111\/jeb.13883","article-title":"Local Adaptation, Geographical Distance and Phylogenetic Relatedness: Assessing the Drivers of Siderophore\u2010Mediated Social Interactions in Natural Bacterial Communities","volume":"34","author":"Butait\u0117 E.","year":"2021","journal-title":"Journal of Evolutionary Biology"},{"key":"e_1_2_10_5_1","doi-asserted-by":"crossref","first-page":"3629","DOI":"10.1111\/1462-2920.14355","article-title":"Environmental Determinants of Pyoverdine Production, Exploitation and Competition in Natural Pseudomonas Communities","volume":"20","author":"Butait\u0117 E.","year":"2018","journal-title":"Environmental Microbiology"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1039\/C8NP00009C","article-title":"Ecology and Evolution of Metabolic Cross\u2010Feeding Interactions in Bacteria","volume":"35","author":"D'Souza G.","year":"2018","journal-title":"Natural Product Reports"},{"key":"e_1_2_10_7_1","doi-asserted-by":"crossref","first-page":"2559","DOI":"10.1111\/evo.12468","article-title":"Less Is 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A.","year":"2010","journal-title":"Conservation Biology"},{"key":"e_1_2_10_12_1","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/s41467-020-14572-x","article-title":"Community Diversity and Habitat Structure Shape the Repertoire of Extracellular Proteins in Bacteria","volume":"11","author":"Garcia\u2010Garcera M.","year":"2020","journal-title":"Nature Communications"},{"key":"e_1_2_10_13_1","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.tim.2016.06.011","article-title":"The Ecology and Evolution of Microbial Competition","volume":"24","author":"Ghoul M.","year":"2016","journal-title":"Trends in Microbiology"},{"key":"e_1_2_10_14_1","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.gde.2015.10.003","article-title":"Microbial Diversity\u2014Exploration of Natural Ecosystems and Microbiomes","volume":"35","author":"Gibbons S. 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Microbiology"},{"key":"e_1_2_10_30_1","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: Recent Updates to the Phylogenetic Tree Display and Annotation Tool","volume":"52","author":"Letunic I.","year":"2024","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_10_31_1","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1111\/2041-210X.13471","article-title":"Phyr: An r Package for Phylogenetic Species\u2010Distribution Modelling in Ecological Communities","volume":"11","author":"Li D.","year":"2020","journal-title":"Methods in Ecology and Evolution"},{"key":"e_1_2_10_32_1","doi-asserted-by":"crossref","first-page":"D1020","DOI":"10.1093\/nar\/gkaa1105","article-title":"RefSeq: Expanding the Prokaryotic Genome Annotation Pipeline Reach With Protein Family Model Curation","volume":"49","author":"Li W.","year":"2021","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_10_33_1","first-page":"E2149","article-title":"Syntrophic Exchange in Synthetic Microbial Communities","volume":"111","author":"Mee M. 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Microbiology"},{"key":"e_1_2_10_55_1","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s13059-021-02295-1","article-title":"Gapseq: Informed Prediction of Bacterial Metabolic Pathways and Reconstruction of Accurate Metabolic Models","volume":"22","author":"Zimmermann J.","year":"2021","journal-title":"Genome Biology"}],"container-title":["Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.70434","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1462-2920.70434","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.70434","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T06:05:12Z","timestamp":1791007512000},"score":1,"resource":{"primary":{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/10.1111\/1462-2920.70434"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":54,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1111\/1462-2920.70434"],"URL":"https:\/\/doi.org\/10.1111\/1462-2920.70434","archive":["Portico"],"relation":{},"ISSN":["1462-2912","1462-2920"],"issn-type":[{"value":"1462-2912","type":"print"},{"value":"1462-2920","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"2026-02-16","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-17","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-02","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70434"}}