{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T03:00:49Z","timestamp":1790910049873,"version":"4.1.0"},"reference-count":73,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T00:00:00Z","timestamp":1765756800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"OCP Nutricrops","award":["AS-85"],"award-info":[{"award-number":["AS-85"]}]},{"DOI":"10.13039\/100016566","name":"UM6P","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100016566","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Peganum harmala (L.) Schrad., a perennial medicinal plant thriving in arid Moroccan soils, represents a natural reservoir of unexplored bacterial diversity. To uncover its hidden foliar endosphere microbiota, we isolated and characterized two Acinetobacter strains: a novel endophytic bacterium, AGC35, and another strain, AGC59, newly reported from this host. Both are non-halophilic, aerobic, Gram-negative bacteria exhibiting optimal growth at 30\u201335 \u00b0C, pH5, and with 1% NaCl. An integrative genomic, phylogenetic, functional, and phenotypic characterization classified both strains within the genus Acinetobacter (class Gamma-pseudomonadota). However, Average Nucleotide Identity (&lt;96%) and digital DNA-DNA Hybridization (&lt;70%) values distinguished the AGC35 strain as a novel species, for which the name Acinetobacter endophylla sp. nov. is proposed. A comparative genomic and phenotypic analysis with the co-isolated Acinetobacter pittii strain AGC59 revealed extensive genome rearrangements, reflecting distinct evolutionary lineage and ecological strategies. While both genomes share core metabolic pathways, A. endophylla harbors specialized genes for the degradation of plant-derived aromatic compounds (e.g., catechol) but shows reduced capacities in carbohydrate metabolism and osmotic stress tolerance, traits indicative of a metabolic specialist with plant-growth-promotion potential, including phosphorus, potassium, and silicon solubilization and indole-3-acetic acid production. In contrast, A. pittii exhibits a more generalist genome enriched in stress functions. Analysis using the Antibiotics and Secondary Metabolite Analysis Shell revealed multiple biosynthetic gene clusters in both strains, showing \u226426% similarity to known references, suggesting the potential for novel antimicrobial secondary metabolite biosynthesis, including antifungal lipopeptides and thiopeptide antibiotics. Altogether, functional specialization and ecological coherence of these findings support the recognition of A. endophylla sp. nov. as a genomically and functionally distinct species, highlighting niche partitioning and adaptive metabolism within the P. harmala holobiont. These results underscore the plant\u2019s value as a reservoir of untapped microbial diversity with significant ecological and biotechnological relevance. Finally, future work will focus on elucidating the novel metabolites encoded by the biosynthetic gene clusters in both isolates and exploring their applications in crop-improvement strategies and natural-product discovery.<\/jats:p>","DOI":"10.3390\/microorganisms13122843","type":"journal-article","created":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T10:11:23Z","timestamp":1765793483000},"page":"2843","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Unveiling Acinetobacter endophylla sp. nov.: A Specialist Endophyte from Peganum harmala with Distinct Genomic and Metabolic Traits"],"prefix":"10.3390","volume":"13","author":[{"given":"Salma","family":"Mouhib","sequence":"first","affiliation":[{"name":"African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khadija","family":"Ait Si Mhand","sequence":"additional","affiliation":[{"name":"African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nabil","family":"Radouane","sequence":"additional","affiliation":[{"name":"African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khaoula","family":"Errafii","sequence":"additional","affiliation":[{"name":"African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1067-1652","authenticated-orcid":false,"given":"Issam","family":"Kadmiri","sequence":"additional","affiliation":[{"name":"Plant and Microbial Biotechnology Center, Agrobiosciences, College of Agriculture and Environmental Sciences, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2651-5884","authenticated-orcid":false,"given":"Derly","family":"Andrade-Molina","sequence":"additional","affiliation":[{"name":"OMICS Sciences Laboratory, Faculty of Health Science, Universidad Esp\u00edritu Santo, Samborond\u00f3n 092301, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Fern\u00e1ndez-Cadena","sequence":"additional","affiliation":[{"name":"OMICS Sciences Laboratory, Faculty of Health Science, Universidad Esp\u00edritu Santo, Samborond\u00f3n 092301, Ecuador"},{"name":"Harvard Medical School, Brigham and Women\u2019s Hospital, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6112-8372","authenticated-orcid":false,"given":"Mohamed","family":"Hijri","sequence":"additional","affiliation":[{"name":"African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco"},{"name":"Institut de Recherche en Biologie V\u00e9g\u00e9tale (IRBV), D\u00e9partement de Sciences Biologiques, Universit\u00e9 de Montr\u00e9al, 4101 Rue Sherbrooke Est., Montr\u00e9al, QC H1X 2B2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1111\/nph.15199","article-title":"Holobiont: A conceptual framework to explore the eco-evolutionary and functional implications of host\u2013microbiota interactions in all ecosystems","volume":"218","author":"Faure","year":"2018","journal-title":"New Phytol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.tim.2008.07.008","article-title":"Properties of bacterial endophytes and their proposed role in plant growth","volume":"16","author":"Hardoim","year":"2008","journal-title":"Trends Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.jare.2019.03.004","article-title":"A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application","volume":"19","author":"Compant","year":"2019","journal-title":"J. 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