{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T17:16:46Z","timestamp":1786123006195,"version":"build-2736575974"},"reference-count":81,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Cadmium (Cd) contamination in the Peruvian Amazon cocoa soils threatens production sustainability and international market access. This study characterized the taxonomic and genomic diversity of bacteria isolated from\n                    <jats:italic>Inga<\/jats:italic>\n                    sp. nodules,\n                    <jats:italic>Quararibea<\/jats:italic>\n                    sp. roots, and rhizosphere soil in cocoa agroforestry systems in Bagua, Amazonas, Peru (1.02\u20133.54\u202fmg Cd kg\n                    <jats:sup>\u22121<\/jats:sup>\n                    ), and evaluated the Cd tolerance phenotypes\n                    <jats:italic>in vitro<\/jats:italic>\n                    . From 93 initial isolates, 53 grew under cadmium screening; 23 were selected for Sanger sequencing, yielding 12 high-quality 16S rRNA sequences suitable for downstream phylogenetic analysis (GenBank: PZ012327\u2013PZ012338). These strains were identified via 16S rRNA gene sequencing and BOX-PCR fingerprinting, revealing distribution across three bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria) and five classes. Notably, no rhizobia sensu stricto were recovered from\n                    <jats:italic>Inga<\/jats:italic>\n                    sp. nodules; all nodule-derived isolates were non-rhizobial endophytes (NREs) belonging to\n                    <jats:italic>Achromobacter<\/jats:italic>\n                    ,\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    ,\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    ,\n                    <jats:italic>Priestia<\/jats:italic>\n                    , and\n                    <jats:italic>Glutamicibacter<\/jats:italic>\n                    . BOX-PCR identified 12 unique genotypes (Shannon H\u2032\u202f=\u202f2.485) distributed in four genomic clusters unrelated to phylogenetic affiliation. The Cd tolerance (25\u2013200\u202fppm) was assessed via OD\u2086\u2080\u2080 in TY medium. Tolerance indices (0.190\u20130.643) classified strains into quartiles: highly tolerant (\n                    <jats:italic>n<\/jats:italic>\n                    \u202f=\u202f3), tolerant (\n                    <jats:italic>n<\/jats:italic>\n                    \u202f=\u202f3), sensitive (\n                    <jats:italic>n<\/jats:italic>\n                    \u202f=\u202f3), and highly sensitive (\n                    <jats:italic>n<\/jats:italic>\n                    \u202f=\u202f3). JSRA_S05 (\n                    <jats:italic>K. va<\/jats:italic>\n                    r\n                    <jats:italic>iicola<\/jats:italic>\n                    ) showed clear hormesis (TI\u202f=\u202f1.235 at 25\u202fppm), whereas JSRA_S08 (\n                    <jats:italic>Glutamicibacter<\/jats:italic>\n                    sp.) exhibited a possible hormetic tendency (TI\u202f=\u202f1.012 at 50\u202fppm). IC\u2085\u2080 values (0.18\u2013719.7\u202fppm) showed low correlation with TI (\n                    <jats:italic>\u03c1<\/jats:italic>\n                    \u202f&amp;lt;\u202f0.1), indicating complementary dimensions of tolerance. Tolerance was strain-specific, as evidenced by opposite responses of two\n                    <jats:italic>K. variicola<\/jats:italic>\n                    strains (highly tolerant JSRA_S05 versus highly sensitive JSRA_N14). Strains associated with\n                    <jats:italic>Quararibea<\/jats:italic>\n                    sp. were consistently among the most tolerant. Three strains (JSRA_S05, JSRA_S08, and JSRA_R15), combining high physiological tolerance with taxonomic and source diversity, are proposed as priority candidates for functional evaluation in biosorption, bioaccumulation, and plant-inoculation assays. These culture-dependent findings indicate that, under the cultivation conditions employed, the cultivable bacterial fraction recovered from Cd-impacted Inga sp. nodules in Amazonian cocoa agroecosystems is dominated by non-rhizobial endophytes, representing a promising biological resource for further bioremediation studies. Whether classical rhizobia are truly absent or simply not retrieved under these conditions requires culture-independent confirmation.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1845000","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T12:47:33Z","timestamp":1786106853000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Cadmium tolerance and taxonomic diversity of cultivable bacteria isolated from Inga sp. nodules, Quararibea sp. roots and rhizosphere soil in cocoa agroforestry systems of the Peruvian Amazon"],"prefix":"10.3389","volume":"17","author":[{"given":"Jessenia Shirley","family":"Ramos Armaulia","sequence":"first","affiliation":[{"name":"Instituto de Investigaci\u00f3n para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodr\u00edguez de Mendoza de Amazonas","place":["Chachapoyas, Amazonas, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santos Triunfo Leiva","family":"Espinoza","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodr\u00edguez de Mendoza de Amazonas","place":["Chachapoyas, Amazonas, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Segundo Manuel Oliva","family":"Cruz","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodr\u00edguez de Mendoza de Amazonas","place":["Chachapoyas, Amazonas, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,7]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cotox.2021.11.001","article-title":"The relevance of hormesis at higher levels of biological organization: hormesis in microorganisms","volume":"29","author":"Agathokleous","year":"2022","journal-title":"Curr. 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