{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T16:01:47Z","timestamp":1791907307632,"version":"4.3.4"},"reference-count":48,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2023,10,26]],"date-time":"2023-10-26T00:00:00Z","timestamp":1698278400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010751","name":"Fondecyt Project","doi-asserted-by":"publisher","award":["11200093"],"award-info":[{"award-number":["11200093"]}],"id":[{"id":"10.13039\/501100010751","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The Region of Arica and Parinacota (Atacama Desert) offers several unexplored remote sites with unique characteristics that would allow for the formulation of new bioproducts for agriculture. Among them, Jurasi Hot Springs, Polloquere Hot Springs, and Amuyo Lagoons represent a group of open pools fed by thermal water springing from the mountains. Their microbiomes remain unspecified, providing a unique opportunity to characterize the endemic community of these sites and develop new bioproducts for sustainable agriculture. Bacteria were isolated from the sediments of these geothermal sites and characterized by sequencing the 16S rRNA gene, microbiological characterization, and agricultural functional characterization. A total of 57 bacteria were isolated from three geothermal sites north of the Atacama Desert. The sequence analysis showed that the isolates belong to several bacterial genera, including Pantoea, Bacillus, and Pseudomonas, among others. The functional characterization revealed the presence of PGP traits, hydrolytic enzymes, and biocontrol activity against phytopathogenic fungi. These bacteria possess the potential to develop new biobased products for agriculture in arid conditions.<\/jats:p>","DOI":"10.3390\/microorganisms11112635","type":"journal-article","created":{"date-parts":[[2023,10,26]],"date-time":"2023-10-26T06:20:16Z","timestamp":1698301216000},"page":"2635","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Isolation and Identification of Bacteria from Three Geothermal Sites of the Atacama Desert and Their Plant-Beneficial Characteristics"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1039-3197","authenticated-orcid":false,"given":"Patricio","family":"Mu\u00f1oz-Torres","sequence":"first","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4743-0924","authenticated-orcid":false,"given":"Sebasti\u00e1n L.","family":"M\u00e1rquez","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Cient\u00edfica y Cultural Biociencia, Jos\u00e9 Domingo Ca\u00f1as, 2280 \u00d1u\u00f1oa, Santiago 7750132, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5610-0970","authenticated-orcid":false,"given":"Germ\u00e1n","family":"Sep\u00falveda-Chavera","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steffany","family":"C\u00e1rdenas-Ninasivincha","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mabel","family":"Arismendi-Macuer","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2321-7416","authenticated-orcid":false,"given":"Wilson","family":"Huanca-Mamani","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yola","family":"Aguilar","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Quezada","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franco","family":"Bugue\u00f1o","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Vegetal y Bioproductos, Facultad de Ciencias Agron\u00f3micas, Universidad de Tarapac\u00e1, Av. General Vel\u00e1squez 1775, Arica 1000000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,10,26]]},"reference":[{"key":"ref_1","unstructured":"(2022, April 25). Three Key Challenges Facing Agriculture and How to Start Solving Them. Available online: https:\/\/www.oecd.org\/agriculture\/key-challenges-agriculture-how-solve\/."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Gupta, V., Sharma, G., Tuohy, M., and Gaur, R. (2016). The Handbook of Microbial Bioresources, CABI. [1st ed.].","DOI":"10.1079\/9781780645216.0000"},{"key":"ref_3","unstructured":"Doelle, H., Rokem, J., and Berovic, M. (2009). Fundamentals in Biotechnology, EOLSS. [1st ed.]."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Aasfas, A., Bargaz, A., Yaakoubi, K., Hilali, A., Bennis, I., Zeroual, Y., and Kadmiri, I. (2021). Nitrogen fixing Azotobacter species as potential soil biological enhancers for crop nutrition and yield stability. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.628379"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Tian, J., Ge, F., Zhang, D., Deng, S., and Liu, X. (2021). Roles of phosphate solubilizing microorganisms from managing phosphorus deficiency to mediating biogeochemical P cycle. Biology, 10.","DOI":"10.3390\/biology10020158"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3984","DOI":"10.1007\/s11356-015-4294-0","article-title":"Microbial siderophores and their potential applications: A review","volume":"23","author":"Saha","year":"2016","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Egamberdieva, D., Wirth, S., Alqarawi, A., Abd_Allah, E., and Hashem, A. (2017). Phytohormones and beneficial microbes: Essential components for plants to balance stress and fitness. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.02104"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Mu\u00f1oz-Torres, P., C\u00e1rdenas, S., Arismendi, M., Huanacuni, N., Huanca-Mamani, W., Cifuentes, D., and Sep\u00falveda-Chavera, G. (2021). The endophytic Pseudomonas sp. S57 for plant-growth promotion and the biocontrol of phytopathogenic fungi and nematodes. Plants, 10.","DOI":"10.3390\/plants10081531"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1146\/annurev-phyto-082712-102340","article-title":"Induced systemic resistance by beneficial microbes","volume":"52","author":"Pieterse","year":"2014","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_10","unstructured":"(2022, April 25). Insights on the Agricultural Biologicals Global Market to 2026. Growing Demand for Food Owing to Booming Population Growth Is Driving the Industry. Available online: https:\/\/www.businesswire.com\/news\/home\/20210510005337\/en\/Insights-on-the-Agricultural-Biologicals-Global-Market-to-2026---Growing-Demand-for-Food-Owing-to-Booming-Population-Growth-is-Driving-the-Industry---ResearchAndMarkets.com."},{"key":"ref_11","first-page":"263","article-title":"Native strains of Trichoderma from northern Chile: Adaptive tolerance in boric saline soils","volume":"40","year":"2015","journal-title":"Interciencia"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1602","DOI":"10.3390\/su2061602","article-title":"Resistance of microorganisms to extreme environmental conditions and its contribution to astrobiology","volume":"2","author":"Rampelotto","year":"2010","journal-title":"Sustainability"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Shilev, S. (2020). Plant-growth-promoting bacteria mitigating soil salinity stress in plants. Appl. Sci., 10.","DOI":"10.3390\/app10207326"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Gaete, A., Mandakovic, D., and Gonz\u00e1lez, M. (2020). Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics. Microorganisms, 8.","DOI":"10.3390\/microorganisms8081213"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1080\/01490451.2021.1879972","article-title":"Isolation and Identification of Extremophilic Bacteria with Potential as Plant Growth Promoters (Pgpb) of A Geothermal Site: A Case Study","volume":"38","year":"2021","journal-title":"Geomicrobiol. J."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"8001","DOI":"10.4238\/2015.July.17.8","article-title":"A simple, fast, and inexpensive CTAB-PVP-silica based method for genomic DNA isolation from single, small insect larvae and pupae","volume":"14","year":"2015","journal-title":"Genet. Mol. Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1128\/AEM.02272-07","article-title":"Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes","volume":"74","author":"Frank","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Criscuolo, A., and Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol., 10.","DOI":"10.1186\/1471-2148-10-210"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_23","first-page":"489","article-title":"Protease producing bacteria and activity in gut of Tiger Shrimp (Penaeus monodon)","volume":"10","author":"Bhowmik","year":"2015","journal-title":"J. Fish. Aquat. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4626","DOI":"10.1128\/JCM.38.12.4626-4628.2000","article-title":"Tween 80 opacity test responses of various Candida species","volume":"38","author":"Slifkin","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"ref_25","first-page":"1186","article-title":"Detection of chitinase on chitin agar plates","volume":"8","author":"Verma","year":"2019","journal-title":"Int. J. Sci. Res."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Hossain, T.J., Chowdhury, S.I., Mozumder, H.A., Chowdhury, M.N.A., Ali, F., Rahman, N., and Dey, S. (2020). Hydrolytic exoenzymes produced by bacteria isolated and identified from the gastrointestinal tract of Bombay Duck. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.02097"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/S0021-9673(00)89300-0","article-title":"The Van Urk-Salkowski reagent-a sensitive and specific chromogenic reagent for silica gel thin-layer chromatographic detection and identification of indole derivatives","volume":"132","author":"Ehmann","year":"1977","journal-title":"J. Chromatogr."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1128\/aem.44.4.990-991.1982","article-title":"Improved medium for isolation of Azospirillum spp.","volume":"44","year":"1982","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_29","first-page":"362","article-title":"Mobilization of phosphorus in soil in connection with the vital activity of some microbial species","volume":"17","author":"Pikovskaya","year":"1948","journal-title":"Microbiologiya"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/0003-2697(87)90612-9","article-title":"Universal chemical assay for the detection and determination of siderophores","volume":"160","author":"Schwynand","year":"1987","journal-title":"Anal. Biochem."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Sep\u00falveda-Chavera, G.F., Arismendi, M., and Mu\u00f1oz-Torres, P. (2020). Endospore-Forming Bacteria Present in a Commercial Stabilized Poultry Manure Determines the Fusarium Biocontrol and the Tomato Growth Promotion. Agronomy, 10.","DOI":"10.3390\/agronomy10111636"},{"key":"ref_32","first-page":"285","article-title":"Recursos h\u00eddricos y desarrollo socioecon\u00f3mico en zonas \u00e1ridas: Importancia y perspectivas de nuevas tecnolog\u00edas aplicadas al tratamiento de aguas naturales y\/o residuales","volume":"17","author":"Cornejo","year":"2009","journal-title":"Ingeniare Rev. Chil. Ing."},{"key":"ref_33","unstructured":"ODEPA (2023, May 22). Regi\u00f3n de Arica y Parinacota: Informaci\u00f3n Regional 2018. Available online: https:\/\/www.odepa.gob.cl\/wp-content\/uploads\/2018\/02\/Arica-y-Parinacota.pdf."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.1111\/mec.14091","article-title":"Introduction: Microbial local adaptation: Insights from natural populations, genomics and experimental evolution","volume":"26","author":"Giraud","year":"2017","journal-title":"Mol. Ecol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1111\/afe.12131","article-title":"Plant-associated Bacillus spp. alter life-history traits of the specialist insect Brevicoryne brassicae L.","volume":"18","author":"Gadhave","year":"2016","journal-title":"Agric. For. Entomol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"12832","DOI":"10.1038\/s41598-019-49216-8","article-title":"Applications of new rhizobacteria Pseudomonas isolates in agroecology via fundamental processes complementing plant growth","volume":"9","author":"Qessaoui","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"206","DOI":"10.5604\/12321966.1203879","article-title":"Pantoea agglomerans: A mysterious bacterium of evil and good. Part IV. Beneficial effects","volume":"23","author":"Dutkiewicz","year":"2016","journal-title":"Ann. Agric. Environ. Med."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Marfet\u00e1n, J., Gallo, A., Farias, M., V\u00e9lez, M., Pescuma, M., and Ordo\u00f1ez, O. (2023). Exiguobacterium sp. as a bioinoculant for plant-growth promotion and Selenium biofortification strategies in horticultural plants. World J. Microbiol. Biotechnol., 39.","DOI":"10.1007\/s11274-023-03571-x"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"115206","DOI":"10.1016\/j.geoderma.2021.115206","article-title":"Oxidases and hydrolases mediate soil organic matter accumulation in chernozem of northeastern China","volume":"403","author":"Wu","year":"2021","journal-title":"Geoderma"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.bjm.2018.03.001","article-title":"Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach","volume":"49","author":"Souza","year":"2018","journal-title":"Braz. J. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1111\/lam.12165","article-title":"Plant growth-promoting potential of bacteria isolated from active volcano sites of Barren Island, India","volume":"58","author":"Amaresan","year":"2013","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Arora, N.K., Mishra, J., and Mishra, V. (2020). Microbial Enzymes: Roles and Applications in Industries, Springer. Microorganisms for Sustainability.","DOI":"10.1007\/978-981-15-1710-5"},{"key":"ref_43","unstructured":"Narasimha-Murthy, K., Soumya, K., Udayashankar, A.C., and Sudisha-Jogaiah, S.C. (2021). Biocontrol Agents and Secondary Metabolites, Woodhead Publishing."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"635","DOI":"10.22376\/ijpbs.2017.8.2.b635-642","article-title":"Optimization of protease production from plant growth promoting Bacillus amyloliquefaciens showing antagonistic activity against phytopathogens","volume":"8","author":"Majumdar","year":"2017","journal-title":"Int. J. Pharm. Bio. Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1007\/s10482-020-01482-7","article-title":"Diversity of culturable bacteria isolated from ancestral crops of Arica and Parinacota Region, Atacama Desert","volume":"113","author":"Arismendi","year":"2020","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref_46","first-page":"1727","article-title":"Antagonistic and plant growth promoting properties of actinomycetes from rhizosphere Deschampsia antarctica \u00c8. Desv. (Galindez Island, Antarctica)","volume":"1","author":"Tistechok","year":"2019","journal-title":"\u0423\u043a\u0440\u0430\u0457\u043d\u0441\u044c\u043a\u0438\u0439 \u0410\u043d\u0442\u0430\u0440\u043a\u0442\u0438\u0447\u043d\u0438\u0439 \u0416\u0443\u0440\u043d\u0430\u043b"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"99","DOI":"10.7324\/JABB.2019.70415","article-title":"Biodiversity of psychrotrophic microbes and their biotechnological applications","volume":"7","author":"Yadav","year":"2019","journal-title":"J. Appl. Biol. Biotechnol."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Govindasamy, V., George, P., Kumar, M., Aher, L., Raina, S.K., Rane, J., Annapurna, K., and Minhas, P.S. (2019). Multi-trait PGP rhizobacterial endophytes alleviate drought stress in a senescent genotype of sorghum [Sorghum bicolor (L.) Moench]. 3 Biotech, 10.","DOI":"10.1007\/s13205-019-2001-4"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/11\/11\/2635\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:12:15Z","timestamp":1760130735000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/11\/11\/2635"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,26]]},"references-count":48,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2023,11]]}},"alternative-id":["microorganisms11112635"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms11112635","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,26]]}}}