{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T03:01:22Z","timestamp":1790910082190,"version":"4.1.0"},"reference-count":51,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T00:00:00Z","timestamp":1777507200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"OCP Nutricrops","award":["Project AS-85"],"award-info":[{"award-number":["Project AS-85"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Endophytic bacteria from plants adapted to arid and semi-arid environments represent an underexplored reservoir of microbial diversity with potential agricultural applications. Here, we report a polyphasic taxonomic and genome-based characterization of Achromobacter sp. isolates recovered from root and foliar tissues of Citrullus colocynthis and Peganum harmala, two medicinal plants thriving under harsh environmental conditions. Whole-genome sequencing, phylogenomic analyses, average nucleotide identity (ANI), digital DNA\u2013DNA hybridization (dDDH), multilocus sequence typing, and detailed phenotypic profiling revealed three previously undescribed species, for which we propose the names Achromobacter colocynthi sp. nov., Achromobacter maghribensis sp. nov., and Achromobacter semiaridum sp. nov. Genome assemblies were highly complete (98.7\u201399.2%) with minimal contamination (&lt;1%), supporting robust taxonomic inference. All three species displayed ANI and dDDH values below accepted thresholds relative to their closest phylogenetic neighbors, despite partial inconsistencies in 16S rRNA similarity for one isolate, highlighting the value of genome-wide metrics for species delineation. Phylogenomic analyses placed the novel taxa within Achromobacter sp. as distinct evolutionary lineages. Phenotypic characterization indicated broad metabolic versatility, including utilization of carbohydrates, organic acids, and amino acids, tolerance to moderate salinity and acidic pH, and resistance to multiple antimicrobial compounds, traits likely linked to adaptation to endophytic lifestyles under semi-arid conditions. Beyond their taxonomic novelty, the isolates exhibited in vitro traits associated with plant adaptation and stress tolerance, including IAA production, ACC deaminase activity, and tolerance to Zn, Cu, and Cd. Genomic analyses further indicated functions related to phosphate acquisition and stress response. These findings expand the taxonomic framework of Achromobacter sp., establish C. colocynthis and P. harmala as reservoirs of novel endophytic bacteria, and highlight their potential relevance for agricultural biotechnology in stress-prone environments.<\/jats:p>","DOI":"10.3390\/microorganisms14051019","type":"journal-article","created":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T12:20:25Z","timestamp":1777551625000},"page":"1019","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genome-Resolved Delineation of Three Novel Endophytic Achromobacter Species from Desert Medicinal Plants"],"prefix":"10.3390","volume":"14","author":[{"given":"Khadija","family":"Ait Si Mhand","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":"Salma","family":"Mouhib","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":"Juan Carlos","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 and 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":[[2026,4,30]]},"reference":[{"key":"ref_1","unstructured":"Washington Colloquium, D. 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