Abstract
Microorganisms showed unique mechanisms to resist and detoxify harmful metals in response to pollution. This study shows the relationship between presence of heavy metals and plant growth regulator compounds. Additionally, the responses of Rhodotorula mucilaginosa YR29 isolated from the rhizosphere of Prosopis sp. growing in a polluted mine jal in Mexico are presented. This research carries out a phenotypic characterization of R. mucilaginosa to identify response mechanisms to metals and confirm its potential as a bioremediation agent. Firstly, Plant Growth-Promoting (PGP) compounds were assayed using the Chrome Azurol S (CAS) medium and the Salkowski method. In addition, to clarify its heavy metal tolerance mechanisms, several techniques were performed, such as optical microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) supplemented with assorted detectors. Scanning transmission electron microscopy (STEM) was used for elementary mapping of the cell. Finally, yeast viability after all treatments was confirmed by confocal laser scanning microscopy (CLSM). The results have suggested that R. mucilaginosa could be a PGP yeast capable of triggering Pb2+ biosorption (representing 22.93% of the total cell surface area, the heavy metal is encapsulated between the cell wall and the microcapsule), and Pb2+ bioaccumulation (representing 11% of the total weight located in the vacuole). Based on these results, R. mucilaginosa as a bioremediation agent and its wide range of useful mechanisms for ecological purposes are highlighted.
Similar content being viewed by others
Data availability
The data material is real, available, and transparent.
References
Adamo GM, Brocca S, Passolunghi S, Salvato B, Lotti M (2012) Laboratory evolution of copper tolerant yeast strains. Microb Cell Fact 11:1
Ahmed E, Holmström SJM (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208. https://doi.org/10.1111/1751-7915.12117
Anahid S, Yaghmaei S, Ghobadinejad Z (2011) Heavy metal tolerance of fungi. Sci Iran 18:502–508. https://doi.org/10.1016/j.scient.2011.05.015
Andersen D, Renshaw JC, Wiebe MG (2003) Rhodotorulic acid production by Rhodotorula mucilaginosa. Mycol Res 107:949–956. https://doi.org/10.1017/S0953756203008220
Arshad M, Frankenberger WT (1997) Plant growth-regulating substances in the rhizosphere: microbial production and functions. Adv Agron 62:45–151. https://doi.org/10.1016/S0065-2113(08)60567-2
Atkin CL, Neilands JB, Phaff HJ (1970) Rhodotorulic acid from species of Leucosporidium, Rhodosporidium, Rhodotorula, Sporidiobolus, and Sporobolomyces, and a new alanine-containing ferrichrome from Cryptococcus melibiosum. J Bacteriol 103:722–733. https://doi.org/10.1128/jb.103.3.722-733.1970
Bau YS (1981) Indole compounds in Saccharomyces cerevisiae and Aspergillus niger. Bot Bull Acad Sin 22:123–130
Bent E (2006) Induced systemic resistance mediated by plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF). In: Tuzun S, Bent E (ed) Multigenic and induced systemic resistance in plants. Springer, Boston, pp 225–258 https://doi.org/10.1007/0-387-23266-4_10
Bozzola JJ, Russel LD (1999) Electron microscopy: principles and techniques for biologists, 2a edn. Jones and Bartlett Press, New York
Braud A, Hoegy F, Jezequel K, Lebeau T, Schalk IJ (2009) New insights into the metal specificity of the Pseudomonas aeruginosa pyoverdine-iron uptake pathway. Environ Microbiol 11:1079–1091. https://doi.org/10.1111/j.1462-2920.2008.01838.x
Chibuike GU, Obiora SC, Chibuike GU, Obiora SC (2014) Heavy metal polluted soils: effect on plants and bioremediation methods. Appl Environ Soil Sci. https://doi.org/10.1155/2014/752708
Cho DH, Kim EY (2003) Characterization of Pb2+ biosorption from aqueous solution by Rhodotorula glutinis. Bioprocess Biosyst Eng 25:271–277. https://doi.org/10.1007/s00449-002-0315-8
Cho DH, Chu KH, Kim EY (2011) Lead uptake and potentiometric titration studies with live and dried cells of Rhodotorula glutinis. World J Microbiol Biotechnol 27:1911. https://doi.org/10.1007/s11274-011-0652-3
Cohen JD, Bandurski RS (1982) Chemistry and physiology of the bound auxins. Annu Rev Plant Physiol 33:403–430. https://doi.org/10.1146/annurev.pp.33.060182.002155
Dary M, Chamber-Pérez MA, Palomares AJ, Pajuelo E (2010) “In situ” phytostabilisation of heavy metal polluted soils using Lupinus luteus inoculated with metal resistant plant-growth promoting rhizobacteria. J Hazard Mater 177:323–330. https://doi.org/10.1016/j.jhazmat.2009.12.035
Deslandes B, Gariépy C, Houde A (2001) Review of microbiological and biochemical effects of skatole on animal production. Livest Prod Sci 71:193–200. https://doi.org/10.1016/S0301-6226(01)00189-0
Glick BR (2003) Phytoremediation: synergistic use of plants and bacteria to clean up the environment. Biotechnol Adv 21:383–393. https://doi.org/10.1016/S0734-9750(03)00055-7
Gordon SA, Weber RP (1951) Colorimetric estimation of indoleacetic acid. Plant Physiol 26:192–195. https://doi.org/10.1104/pp.26.1.192
Hipol RM (2014) Antioxidant potentials of culturable endophytic yeasts from Phragmites australis Cav. (Trin) ex Steud. from copper-contaminated mining site in Mankayan, Benguet. Philipp Sci Lett 14:337
Hong JW, Park JY, Gadd GM (2010) Pyrene degradation and copper and zinc uptake by Fusarium solani and Hypocrea lixii isolated from petrol station soil. J Appl Microbiol 108:2030–2040. https://doi.org/10.1111/j.1365-2672.2009.04613.x
Huang M, Zhu H, Zhang J, Tang D, Han X, Chen L, Du D, Yao J, Chen K, Sun J (2017) Toxic effects of cadmium on tall fescue and different responses of the photosynthetic activities in the photosystem electron donor and acceptor sides. Sci Rep 7:14387. https://doi.org/10.1038/s41598-017-14718-w
Ilyas S, Rehman A, Coelho AV, Sheehan D (2016) Proteomic analysis of an environmental isolate of Rhodotorula mucilaginosa after arsenic and cadmium challenge: Identification of a protein expression signature for heavy metal exposure. J Proteomics 141:47–56. https://doi.org/10.1016/j.jprot.2016.04.012
Kawano T (2003) Roles of the reactive oxygen species-generating peroxidase reactions in plant defense and growth induction. Plant Cell Rep 21:829–837. https://doi.org/10.1007/s00299-003-0591-z
Khan AA, Jilani G, Akhtar MS, Saqlan SM, Rasheed M (2009) Phosphorus solubilizing bacteria: occurrence, mechanisms, and their role in crop production. J Agric Biol Sci 1:48–58
Kraepiel AML, Bellenger JP, Wichard T, Morel FMM (2009) Multiple roles of siderophores in free-living nitrogen-fixing bacteria. Biometals 22:573–581. https://doi.org/10.1007/s10534-009-9222-7
Krishnamoorthy R, Venkateswaran V, Senthilkumar M, Anandham R, Selvakumar G, Kiyoon K, Yeongyong KTS (2017) Potential microbiological approaches for the remediation of heavy metal-contaminated soils. In: Singh D, Singh H, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives. Springer, Singapore, pp 341–366. https://doi.org/10.1007/978-981-10-6593-4_1
Ksheminska H, Fedorovych D, Babyak L, Yanovych D, Kaszycki P, Koloczek H (2005) Chromium (III) and (VI) tolerance and bioaccumulation in yeast: a survey of cellular chromium content in selected strains of representative genera. Process Biochem 40:1565–1572. https://doi.org/10.1016/j.procbio.2004.05.012
Kumar A, Bisht B, Joshi V, Dhewa T (2011) Review on bioremediation of polluted environment: a management tool. Int J Environ Sci 6:1079–1093
Kumar R, Nongkhlaw M, Acharya C, Joshi SR (2013) Growth media composition and heavy metal tolerance behavior of bacteria characterized from the sub-surface soil of uranium rich ore bearing site of Domiasiat in Meghalaya. Indian J Biotechnol 12:115–119
Lampis S, Santi C, Ciurli A, Andreolli M, Vallini G (2015) Promotion of arsenic phytoextraction efficiency in the fern Pteris vittata by the inoculation of As-resistant bacteria: a soil bioremediation perspective. Front Plant Sci 6:80. https://doi.org/10.3389/fpls.2015.00080
Leveau JHJ, Lindow SE (2005) Utilization of the plant hormone indole-3-acetic acid for growth by Pseudomonas putida strain 1290. Appl Environ Microbiol 71:2365–2371. https://doi.org/10.1128/AEM.71.5.2365-2371.2005
Li HY, Li DW, He CM, Zhou ZP, Mei T, Xu HM (2012) Diversity and heavy metal tolerance of endophytic fungi from six dominant plant species in a Pb–Zn mine wasteland in China. Fungal Ecol 5:309–315. https://doi.org/10.1016/j.funeco.2011.06.002
Li J, Jiang Z, Chen S, Wang T, Jiang L, Wang M, Li Z (2019) Biochemical changes of polysaccharides and proteins within EPS under Pb (II) stress in Rhodotorula mucilaginosa. Ecotoxicol Environ Saf 174:484–490. https://doi.org/10.1016/j.ecoenv.2019.03.004
Mandal BK, Suzuki KT (2002) Arsenic round the world: a review. Talanta 58:201–235. https://doi.org/10.1016/S0039-9140(02)00268-0
Mendoza-Hernández JC, Perea-Vélez YS, Arriola-Morales J, Martínez-Simón SM, Pérez-Osorio G (2016) Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria. Microbiol Res 188:53–61. https://doi.org/10.1016/j.micres.2016.05.001
Moliné M, Flores MR, Libkind D, del Carmen DM, Farías ME, van Broock M (2010) Photoprotection by carotenoid pigments in the yeast Rhodotorula mucilaginosa: the role of torularhodin. Photochem Photobiol Sci 9:1145–1151. https://doi.org/10.1039/c0pp00009d
Mostofa MG, Hossain MA, Fujita M, Tran LSP (2015) Physiological and biochemical mechanisms associated with trehalose-induced copper-stress tolerance in rice. Sci Rep 5:11433. https://doi.org/10.1038/srep11433
Mujahid M, Sasikala C, Ramana CV (2011) Production of indole-3-acetic acid and related indole derivatives from L-tryptophan by Rubrivivax benzoatilyticus JA2. Appl Microbiol Biotechnol 89:1001–1008. https://doi.org/10.1007/s00253-010-2951-2
Nassar AH, El-Tarabily KA, Sivasithamparam K (2005) Promotion of plant growth by an auxin-producing isolate of the yeast Williopsis saturnus endophytic in maize (Zea mays L.) roots. Biol Fertil Soils 42:97–108. https://doi.org/10.1007/s00374-005-0008-y
Nutaratat P, Srisuk N, Arunrattiyakorn P, Limtong S (2016) Indole-3-acetic acid biosynthetic pathways in the basidiomycetous yeast Rhodosporidium paludigenum. Arch Microbiol 198:429–437. https://doi.org/10.1007/s00203-016-1202-z
Omran RG (1977) The direct involvement of hydrogen peroxide in indoleacetic acid inactivation. Biochem Biophys Res Commun 78:970–976. https://doi.org/10.1016/0006-291X(77)90516-2
Prathap M, Ranjitha Kumari B (2015) Plant pathology & microbiology a critical review on plant growth promoting rhizobacteria. J Plant Pathol Microbiol 6:4. https://doi.org/10.4172/2157-7471.1000266
Rajendran P, Muthukrishnan J, Gunasekaran P (2003) Microbes in heavy metal remediation. Indian J Exp Biol 41:935–944
Ramos-Garza J, Bustamante-Brito R, Ángeles de Paz G, Medina-Canales MG, Vásquez-Murrieta MS, Wang ET, Rodríguez-Tovar AV (2016) Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils. Can J Microbiol 62:307–319
Ramsay LM, Gadd GM (1997) Mutants of Saccharomyces cerevisiae defective in vacuolar function confirm a role for the vacuole in toxic metal ion detoxification. FEMS Microbiol Lett 152:293–298. https://doi.org/10.1111/j.1574-6968.1997.tb10442.x
Rao RP, Hunter A, Kashpur O, Normanly J (2010) Aberrant synthesis of indole-3-acetic acid in Saccharomyces cerevisiae triggers morphogenic transition, a virulence trait of pathogenic fungi. Genetics 185:211–220. https://doi.org/10.1534/genetics.109.112854
Rathaur P, Ramteke PW, Raja W, John SA (2012) Isolation and characterization of nickel and cadmium tolerant plant growth promoting rhizobacteria from rhizosphere of Withania somnifera. J Biol Environ Sci 6:253–261
Rathnayake IVN, Megharaj M, Krishnamurti GSR, Bolan NS, Naidu R (2013) Heavy metal toxicity to bacteria—are the existing growth media accurate enough to determine heavy metal toxicity? Chemosphere 90:1195–1200. https://doi.org/10.1016/j.chemosphere.2012.09.036
Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56. https://doi.org/10.1016/0003-2697(87)90612-9
Seidel C, Walz A, Park S, Cohen JD, Ludwig-Müller J (2006) Indole-3-acetic acid protein conjugates: novel players in auxin homeostasis. Plant Biol 8:340–345. https://doi.org/10.1055/s-2006-923802
Shoresh M, Harman GE, Mastouri F (2010) Induced systemic resistance and plant responses to fungal biocontrol agents. Annu Rev Phytopathol 48:21–43. https://doi.org/10.1146/annurev-phyto-073009-114450
Spaepen S, Vanderleyden J, Remans R (2007) Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 31:425–448. https://doi.org/10.1111/j.1574-6976.2007.00072.x
Spain Alm E (2003) Implications of microbial heavy metal tolerance in the environment. Rev Undergrad Res 2:1–6
Tognetti VB, Mühlenbock P, van Breusegem F (2012) Stress homeostasis—the redox and auxin perspective. Plant, Cell Environ 35:321–333. https://doi.org/10.1111/j.1365-3040.2011.02324.x
Tromas A, Perrot-Rechenmann C (2010) Recent progress in auxin biology. CR Biol 333:297–306. https://doi.org/10.1016/j.crvi.2010.01.005
Vadkertiová R, Sláviková E (2006) Metal tolerance of yeasts isolated from water, soil, and plant environments. J Basic Microbiol 46:145–152. https://doi.org/10.1002/jobm.200510609
Vazquez-Nin G, Echeverria O (2000) Microscopía Electrónica de barrido aplicada a las ciencias biológicas. Fondo de Cultura Económica, CDMX, México, p 92–117
Villegas LB, Amoroso MJ, de Figueroa LIC (2009) Responses of Candida fukuyamaensis RCL-3 and Rhodotorula mucilaginosa RCL-11 to copper stress. J Basic Microbiol 49:395–403. https://doi.org/10.1002/jobm.200800218
Wang W, Li H, Lin X, Wang Z, Fang B (2017) Identification and characterization of miRNAs involved in adventitious branches formation of Gracilaria lichenoides in vitro. J Appl Phycol 29:607–615. https://doi.org/10.1007/s10811-016-0930-4
Wang M, Ma J, Wang X, Wang Z, Tang L, Chen H, Li Z (2020) Detoxification of Cu (II) by the red yeast Rhodotorula mucilaginosa: from extracellular to intracellular. Appl Microbiol Biotechnol 104:10181–10190. https://doi.org/10.1007/s00253-020-10952-x
Wang Z, Zhang Y, Jiang L, Qiu J, Gao Y, Gu T, Li Z (2021) Responses of Rhodotorula mucilaginosa under Pb (II) stress: carotenoid production and budding. Environ Microbiol 24:678–688. https://doi.org/10.1111/1462-2920.15603
Wasi S, Jeelani G, Ahmad M (2008) Biochemical characterization of a multiple heavy metal, pesticides and phenol resistant Pseudomonas fluorescens strain. Chemosphere 71:1348–1355. https://doi.org/10.1016/j.chemosphere.2007.11.023
Woodward AW, Bartel B (2005) Auxin: regulation, action, and interaction. Ann Bot 95:707–735. https://doi.org/10.1093/aob/mci083
Xin G, Glawe D, Doty SL (2009) Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees. Mycol Res 113:973–980. https://doi.org/10.1016/j.mycres.2009.06.001
Zhang N, Fan Y, Li C, Wang Q, Leksawasdi N, Li F, Wang S (2018) Cell permeability and nuclear DNA staining by propidium iodide in basidiomycetous yeasts. Appl Microbiol Biotechnol 102:4183–4191. https://doi.org/10.1007/s00253-018-8906-8
Acknowledgements
We thank M. en C. Héctor Francisco-Mendoza Leon (Laboratory of Ultra-High-Resolution Scanning Electron Microscopy, CNMN-IPN), Dra. María de Jesús Perea-Flores (Laboratory of Confocal Laser Scanning Microscopy, CNMN-IPN), and Dr. Raúl Borja Urbi (Laboratory of Atomic Resolution Transmission Electron Microscopy, CNMN-IPN) for their support with the SEM, TEM, CSLM and STEM micrographs. AVRT and MGMC were the tutors of GAP. GAP is a CONACyT and BEIFI fellow; AVRT, MGMC and EOLV are COFAA, EDI and SNI fellows. This work was edited by American Journal Experts.
Funding
Part of this work was supported by the “Secretaria de Investigación y Posgrado, del Instituto Politécnico Nacional” projects SIP-IPN 20211222, 20221010, 20220564 and 20230236.
Author information
Authors and Affiliations
Contributions
GAP carried out the experimentation and drafted the first draft of the manuscript. GAP and EOLV processed and interpreted yeast samples for TEM. GAP, MGMC and HMG processed and interpreted yeast samples for SEM and STEM. AVRT and MGMC conceived the original idea, supervised the project, and contributed analyze, write, and edit the final manuscript, ARG write and edit the final manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors have no relevant financial, declare no competing interests.
Ethical approval
No human or animal participants were involved in this study. This is an observational study.
Consent to publish
All authors have read and approved the final manuscript.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
11274_2023_3675_MOESM1_ESM.tiff
Supplementary file1 FigS1 Standard curve of Indole Acetic Acid (µg/mL). The discontinuous line highlights the 95% confidence intervals. Statistical analysis was performed by linear regression, with a significant difference set at a p value of <0.05 (TIFF 3604 KB)
11274_2023_3675_MOESM2_ESM.tiff
Supplementary file2 Viability of Rhodotorula mucilaginosa grown in YNB broth supplemented with different heavy metals (CLSM). This imagen indicates colocalization of cell signals for propidium iodide (IP) and calcofluor white (CFW), corresponding to death cells (1000X) (TIFF 22509 KB)
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Angeles de Paz, G., Martínez-Gutierrez, H., Ramírez-Granillo, A. et al. Rhodotorula mucilaginosa YR29 is able to accumulate Pb2+ in vacuoles: a yeast with bioremediation potential. World J Microbiol Biotechnol 39, 238 (2023). https://doi.org/10.1007/s11274-023-03675-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11274-023-03675-4