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In plant-pathogenic\n                      <jats:italic toggle=\"yes\">Pseudomonas<\/jats:italic>\n                      , certain specialized metabolites can enhance colonization of plant hosts, yet their broader contribution to plant\u2013microbe interactions and the relative importance of different metabolites remain unclear. Specialized metabolites are products of enzymes encoded in biosynthetic gene clusters (BGCs), whose prediction from genome sequences has become routine but whose functional roles are rarely tested experimentally. Here, we characterize the BGC repertoire of 225\n                      <jats:italic toggle=\"yes\">P. viridiflava<\/jats:italic>\n                      isolates from\n                      <jats:italic toggle=\"yes\">Arabidopsis thaliana<\/jats:italic>\n                      and assess BGC contributions to fitness and disease severity\n                      <jats:italic toggle=\"yes\">in planta<\/jats:italic>\n                      . The BGC landscape of\n                      <jats:italic toggle=\"yes\">P. viridiflava<\/jats:italic>\n                      was dominated by non-ribosomal peptide synthetase (NRPS) and NRPS-like BGCs, which accounted for 50% of the predicted BGCs. One-third of the BGC families were restricted to a single isolate. Transposon mutagenesis coupled with random barcode transposon sequencing (RB-TnSeq) revealed that the majority of BGCs reduce rather than increase fitness during\n                      <jats:italic toggle=\"yes\">A. thaliana<\/jats:italic>\n                      infection, with the magnitude of the fitness cost varying across host genotypes. This cost could be due to exploitation of public goods by cheater mutant strains. In single-isolate plant infections, where public goods are not available, we found 11\/34 BGC families correlated with disease severity. Yet, only two of these (an N-acetylglutaminylglutamine amide [NAGGN] and an NRPS) were negatively associated with disease severity, which is positively correlated with bacterial growth in this pathosystem, further indicating that BGCs are generally not beneficial\n                      <jats:italic toggle=\"yes\">in planta<\/jats:italic>\n                      . Our findings reveal extensive and largely uncharacterized biosynthetic potential in populations of\n                      <jats:italic toggle=\"yes\">P. viridiflava<\/jats:italic>\n                      and indicate that candidate metabolites are likely not adaptive for direct interactions with the plant, but perhaps for microbe-microbe interactions either\n                      <jats:italic toggle=\"yes\">in planta<\/jats:italic>\n                      or in other ecological niches.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Bacteria, including plant-associated bacteria such as\n                      <jats:italic toggle=\"yes\">Pseudomonas viridiflava<\/jats:italic>\n                      , produce a vast array of chemical compounds, called secondary or specialized metabolites, that can mediate their interaction with the plant host or other microorganisms. Some of these compounds are known to directly influence how bacteria interact with plants, but it has been unclear whether this is a general rule. We studied a large collection of closely related leaf-dwelling\n                      <jats:italic toggle=\"yes\">P. viridiflava<\/jats:italic>\n                      \u2014a plant pathogen\u2014that varied in their ability to cause disease. We found that very few of the gene clusters responsible for making specialized metabolites improved the ability of the bacteria to colonize its natural host\n                      <jats:italic toggle=\"yes\">Arabidopsis thaliana<\/jats:italic>\n                      . On the contrary, carrying these gene clusters often reduced bacterial growth and disease severity in plants. Specialized metabolites may instead primarily be important for interacting with other microbes, different host species, or under environmental conditions we did not test. These are questions that remain for future research.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00212-26","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T13:00:55Z","timestamp":1781528455000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Biosynthetic gene clusters in\n                    <i>Pseudomonas viridiflava<\/i>\n                    have a fitness cost during\n                    <i>Arabidopsis thaliana<\/i>\n                    infection"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7821-9737","authenticated-orcid":false,"given":"Alejandra","family":"Duque-Jaramillo","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0243gzr89","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Molecular Biology, Max Planck Institute for Biology 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