Endophytic bacterium Sphingomonas sp. SaMR12 facilitates photosynthetic responses to cadmium stress in Brassica juncea L.

Abstract

Plant growth-promoting bacteria (PGPB) are recently acknowledged as an effective eco-friendly agent for plant growth, accumulation and remediation of cadmium (Cd). PGPB isolated from the hyperaccumulator Sedum alfredii Hance were beneficial to Cd phytoextraction by regulating photosynthetic system of Brassica juncea L. However, the intrinsic regulating mechanism of the photosystem and the related key genes and pathways remain unclear. Results of laser scanning confocal microscopy (LSCM) indicated that, for Sphingomonas sp. SaMR12 to successfully survive and colonize in B. juncea they must first invade the base of lateral roots. SaMR12 inoculation under 1 × 10⁻⁵ mol/L Cd significantly increased chlorophyll a contents by 71.98%, ETR by 27.96%, Fv/Fm by 14.17%, \mathrm{\Phi } PS II by 27.96%, qN by 12.67%, and qL by 34.87%, accordingly, indicating that SaMR12 could ameliorate repressive effects by improving the acquisition efficiency of light energy in the chloroplasts, activating the photocatalytic abilities of PS II and the energy cycle of the photosynthetic reaction center. Furthermore, results of RNA sequencing combined with weighed gene co-expression network analysis (WGCNA) identified module ‘ME130’ with 227 genes and ‘ME157’ with 2208 genes were significantly associated with chlorophyll fluorescence parameters, molecular function of these candidate genes mainly categorized to catalytic activity (GO:0003824), binding (GO:0005488), and ATP-dependent activity (GO:0140657); and biological process of these genes mainly fall into cellular process (GO:0009987) and metabolic process (GO:0008152). This study extends the investigation into PGPB functional mechanisms towards Cd accumulation and simultaneously improves acknowledgments of microbe-plant interaction in mitigating contaminants to further guarantee soil health and food safety.

Graphical abstract

Keywords

Cd / Transcriptomic analysis / Gene network / Photosynthesis / Oilseed rape

Highlight

	● The inoculation of Sphingomonas sp. SaMR12 is beneficial for Cd phytoextraction.
	● The inoculation of SaMR12 could alleviate the photosynthetic damage caused by Cd.
	● Two key modules associated with photosystem response under Cd stress were identified.

References

[1] Branca J J V, Pacini A, Gulisano M, Taddei N, Fiorillo C, Becatti M. (2020). Cadmium-induced cytotoxicity: effects on mitochondrial electron transport chain. Frontiers in Cell and Developmental Biology, 8: 604377

[2] Carlos L O, Sun M M, Balcázar J L. (2024). Unraveling the interaction between soil microbiomes and their potential for restoring polluted soils. Frontiers of Environmental Science & Engineering, 18(8): 104

[3] Chalhoub B, Denoeud F, Liu S Y, Parkin I A P, Tang H B, Wang X Y, Chiquet J, Belcram H, Tong C B, Samans B. . (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345(6199): 950–953

[4] Chen B, Shen J G, Zhang X C, Pan F S, Yang X E, Feng Y. (2014). The endophytic bacterium, Sphingomonas SaMR12, improves the potential for zinc phytoremediation by its host, Sedum alfredii. PLoS One, 9(9): e106826

[5] Chen H C, Zhang S L, Wu K J, Li R, He X R, He D N, Huang C, Wei H. (2020a). The effects of exogenous organic acids on the growth, photosynthesis and cellular ultrastructure of Salix variegata Franch. under Cd stress. Ecotoxicology and Environmental Safety, 187: 109790

[6] Chen L, Long C, Wang D, Yang J Y. (2020b). Phytoremediation of cadmium (Cd) and uranium (U) contaminated soils by Brassica juncea L. enhanced with exogenous application of plant growth regulators. Chemosphere, 242: 125112

[7] Chi Y W, Ma X Z, Wu J Q, Wang R Y, Zhang X, Chu S H, Zhang D, Zhou P. (2023). Plant growth promoting endophyte promotes cadmium accumulation in Solanum nigrum L. by regulating plant homeostasis. Journal of Hazardous Materials, 457: 131866

[8] Chu C H, Zhu L Z. (2024). Paving the way toward soil safety and health: current status, challenges, and potential solutions. Frontiers of Environmental Science & Engineering, 18(6): 74

[9] da Silva Oliveira C E, Jalal A, Aguilar J V, De Camargos L S, Zoz T, Ghaley B B, Abdel-Maksoud M A, Alarjani K M, Abdelgawad H, Teixeira Filho M C M. (2023). Yield, nutrition, and leaf gas exchange of lettuce plants in a hydroponic system in response to Bacillus subtilis inoculation. Frontiers in Plant Science, 14: 1248044

[10] Dolu H, Killi D, Bas S, Bilecen D S, Seymen M. (2025). Effectiveness of salt priming and plant growth-promoting bacteria in mitigating salt-induced photosynthetic damage in melon. Photosynthesis Research, 163(1): 7

[11] Figlioli F, Sorrentino M C, Memoli V, Arena C, Maisto G, Giordano S, Capozzi F, Spagnuolo V. (2019). Overall plant responses to Cd and Pb metal stress in maize: growth pattern, ultrastructure, and photosynthetic activity. Environmental Science and Pollution Research, 26(2): 1781–1790

[12] Hao X Y, Li J P, Gao S Q, Tuerxun Z, Chang X C, Hu W R, Chen G, Huang Q S. (2020). SsPsaH, a H subunit of the photosystem I reaction center of Suaeda salsa, confers the capacity of osmotic adjustment in tobacco. Genes & Genomics, 42(12): 1455–1465

[13] Hou Y R, Zhao Y Y, Lu J L, Wei Q Q, Zang L B, Zhao X Y. (2023). Environmental contamination and health risk assessment of potentially toxic trace metal elements in soils near gold mines - A global meta-analysis. Environmental Pollution, 330: 121803

[14] Hu T, Wang T, Wang G Y, Bi A Y, Wassie M, Xie Y, Xu H W, Chen L. (2021). Overexpression of FaHSP17.8-CII improves cadmium accumulation and tolerance in tall fescue shoots by promoting chloroplast stability and photosynthetic electron transfer of PSII. Journal of Hazardous Materials, 417: 125932

[15] Jia L, Yu G C, Zhao Z, Lü L L. (2025). Effects of cadmium (Cd) on photosynthetic characteristics and chlorophyll fluorescence parameters in the ornamental Plant Salvia splendens Ker-Gawl. Physiology and Molecular Biology of Plants, 31(3): 507–519

[16] Khan K Y, Ali B, Stoffella P J, Cui X Q, Yang X E, Guo Y. (2020). Study amino acid contents, plant growth variables and cell ultrastructural changes induced by cadmium stress between two contrasting cadmium accumulating cultivars of Brassica rapa ssp. chinensis L. (pak choi). Ecotoxicology and Environmental Safety, 200: 110748

[17] Kumar A, Kumari N, Singh A, Kumar D, Yadav D K, Varshney A, Sharma N. (2023). The effect of cadmium tolerant plant growth promoting rhizobacteria on plant growth promotion and phytoremediation: a review. Current Microbiology, 80(5): 153

[18] Kurniawan S B, Ramli N N, Said N S M, Alias J, Imron M F, Abdullah S R S, Othman A R, Purwanti I F, Hasan H A. (2022). Practical limitations of bioaugmentation in treating heavy metal contaminated soil and role of plant growth promoting bacteria in phytoremediation as a promising alternative approach. Heliyon, 8(4): e08995

[19] Langfelder P, Horvath S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9(1): 559

[20] Liu Z G, Wu X Z, Hou L, Ji S Z, Zhang Y, Fan W R, Li T, Zhang L, Liu P, Yang L. (2023). Effects of cadmium on transcription, physiology, and ultrastructure of two tobacco cultivars. Science of the Total Environment, 869: 161751

[21] Livak K J, Schmittgen T D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the method. Methods, 25(4): 402–408

[22] Lysenko E A, Klaus A A, Kartashov A V, Kusnetsov V V. (2020). Specificity of Cd, Cu, and Fe effects on barley growth, metal contents in leaves and chloroplasts, and activities of photosystem I and photosystem II. Plant Physiology and Biochemistry, 147: 191–204

[23] Ma C, Wang M L, Li Q, Vakili M, Zhang Y J, Hei S Q, Gao L, Wang W, Liu D C. (2025). Distribution, source apportionment, and assessment of heavy metal pollution in the Yellow River Basin, Northwestern China. Frontiers of Environmental Science & Engineering, 19(2): 16

[24] Mai X, Tang J, Tang J X, Zhu X Y, Yang Z H, Liu X, Zhuang X J, Feng G, Tang L. (2025). Research progress on the environmental risk assessment and remediation technologies of heavy metal pollution in agricultural soil. Journal of Environmental Sciences, 149: 1–20

[25] Moran R, Porath D. (1980). Chlorophyll determination in intact tissues using N,N-dimethylformamide. Plant Physiology, 65(3): 478–479

[26] Ohashi-Ito K, Iwamoto K, Fukuda H. (2024). LONESOME HIGHWAY-TARGET OF MONOPTEROS5 transcription factor complex promotes a predifferentiation state for xylem vessel differentiation in the root apical meristem by inducing the expression of VASCULAR-RELATED NAC-DOMAIN genes. New Phytologist, 242(3): 1146–1155

[27] Ozfidan-KonakciCArikanBAlp-Turgut F NBalciMUysalAYildiztugay E (2023). Halotolerant plant growth-promoting bacteria, Bacillus pumilus, modulates water status, chlorophyll fluorescence kinetics and antioxidant balance in salt and/or arsenic-exposed wheat. Environmental Research, 231(Pt 1): 116089

[28] Pan F S, Luo S, Shen J, Wang Q, Ye J Y, Meng Q, Wu Y J, Chen B, Cao X R, Yang X E. . (2017). The effects of endophytic bacterium SaMR12 on Sedum alfredii Hance metal ion uptake and the expression of three transporter family genes after cadmium exposure. Environmental Science and Pollution Research, 24(10): 9350–9360

[29] Pan F S, Meng Q, Wang Q, Luo S, Chen B, Khan K Y, Yang X E, Feng Y. (2016). Endophytic bacterium Sphingomonas SaMR12 promotes cadmium accumulation by increasing glutathione biosynthesis in Sedum alfredii Hance. Chemosphere, 154: 358–366

[30] Park E J, Kim T H. (2021). Arabidopsis OSMOTIN 34 functions in the ABA signaling pathway and is regulated by proteolysis. International Journal of Molecular Sciences, 22(15): 7915

[31] Peng J Y, Zhang S, Han Y Y, Bate B, Ke H, Chen Y M. (2022). Soil heavy metal pollution of industrial legacies in China and health risk assessment. Science of the Total Environment, 816: 151632

[32] Peršić V, Antunović Dunić J, Domjan L, Zellnig G, Cesar V. (2022). Time course of age-linked changes in photosynthetic efficiency of Spirodela polyrhiza exposed to cadmium. Frontiers in Plant Science, 13: 872793

[33] Rahimi S, Talebi M, Baninasab B, Gholami M, Zarei M, Shariatmadari H. (2020). The role of plant growth-promoting rhizobacteria (PGPR) in improving iron acquisition by altering physiological and molecular responses in quince seedlings. Plant Physiology and Biochemistry, 155: 406–415

[34] Raza A, Habib M, Kakavand S N, Zahid Z, Zahra N, Sharif R, Hasanuzzaman M. (2020). Phytoremediation of cadmium: physiological, biochemical, and molecular mechanisms. Biology, 9(7): 177

[35] Rosca M, Cozma P, Minut M, Hlihor R M, Bețianu C, Diaconu M, Gavrilescu M. (2021). New evidence of model crop Brassica napus L. in soil clean-up: comparison of tolerance and accumulation of lead and cadmium. Plants, 10(10): 2051

[36] Ru S H, Wang J Q, Su D C. (2004). Characteristics of Cd uptake and accumulation in two Cd accumulator oilseed rape species. Journal of Environmental Sciences, 16(4): 594–598

[37] Sagonda T, Adil M F, Sehar S, Rasheed A, Joan H I, Ouyang Y N, Shamsi I H. (2021). Physio-ultrastructural footprints and iTRAQ-based proteomic approach unravel the role of Piriformospora indica-colonization in counteracting cadmium toxicity in rice. Ecotoxicology and Environmental Safety, 220: 112390

[38] Santander R D, Català-Senent J F, Figàs-Segura À, Biosca E G. (2020). From the roots to the stem: unveiling pear root colonization and infection pathways by Erwinia amylovora. FEMS Microbiology Ecology, 96(12): fiaa210

[39] Seneviratne M, Rajakaruna N, Rizwan M, Madawala H M S P, Ok Y S, Vithanage M. (2019). Heavy metal-induced oxidative stress on seed germination and seedling development: a critical review. Environmental Geochemistry and Health, 41(4): 1813–1831

[40] Shahid M, Javed M T, Masood S, Akram M S, Azeem M, Ali Q, Gilani R, Basit F, Abid A, Lindberg S. (2019). Serratia sp. CP-13 augments the growth of cadmium (Cd)-stressed Linum usitatissimum L. by limited Cd uptake, enhanced nutrient acquisition and antioxidative potential. Journal of Applied Microbiology, 126(6): 1708–1721

[41] Shen C, Huang Y Y, Liao Q, Huang B F, Xin J L, Wang L, Fu H L. (2023). Characterization of cadmium accumulation mechanism between eggplant (Solanum melongena L.) cultivars. Frontiers in Plant Science, 13: 1097998

[42] Sperdouli I, Adamakis I D S, Dobrikova A, Apostolova E, Hanć A, Moustakas M. (2022). Excess zinc supply reduces cadmium uptake and mitigates cadmium toxicity effects on chloroplast structure, oxidative stress, and photosystem II photochemical efficiency in Salvia sclarea plants. Toxics, 10(1): 36

[43] Su D C, Wong J W C. (2004). Selection of mustard oilseed rape (Brassica juncea L.) for phytoremediation of cadmium contaminated soil. Bulletin of Environmental Contamination and Toxicology, 72(5): 991–998

[44] Su F, Zhao B, Dhondt-Cordelier S, Vaillant-Gaveau N. (2024). Plant-growth-promoting rhizobacteria modulate carbohydrate metabolism in connection with host plant defense mechanism. International Journal of Molecular Sciences, 25(3): 1465

[45] Taj Z, Challabathula D. (2021). Protection of photosynthesis by halotolerant Staphylococcus sciuri ET101 in tomato (Lycoperiscon esculentum) and rice (Oryza sativa) plants during salinity stress: possible interplay between carboxylation and oxygenation in stress mitigation. Frontiers in Microbiology, 11: 547750

[46] Thanwisai L, Tran H T K, Siripornadulsil W, Siripornadulsil S. (2022). A cadmium-tolerant endophytic bacterium reduces oxidative stress and Cd uptake in KDML105 rice seedlings by inducing glutathione reductase-related activity and increasing the proline content. Plant Physiology and Biochemistry, 192: 72–86

[47] Trapnell C, Williams B A, Pertea G, Mortazavi A, Kwan G, Van Baren M J, Salzberg S L, Wold B J, Pachter L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28(5): 511–515

[48] Tsai H H, Wang J C, Geldner N, Zhou F. (2023). Spatiotemporal control of root immune responses during microbial colonization. Current Opinion in Plant Biology, 74: 102369

[49] Wang C C, Zhang Q C, Yan C A, Tang G Y, Zhang M Y, Ma L Q, Gu R H, Xiang P. (2023). Heavy metal(loid)s in agriculture soils, rice, and wheat across China: status assessment and spatiotemporal analysis. Science of the Total Environment, 882: 163361

[50] Wang Q, Ge C F, Xu S A, Wu Y J, Sahito Z A, Ma L Y, Pan F S, Zhou Q Y, Huang L K, Feng Y. . (2020). The endophytic bacterium Sphingomonas SaMR12 alleviates Cd stress in oilseed rape through regulation of the GSH-AsA cycle and antioxidative enzymes. BMC Plant Biology, 20(1): 63

[51] Wang Q, Ma L Y, Zhou Q Y, Chen B, Zhang X C, Wu Y J, Pan F S, Huang L K, Yang X E, Feng Y. (2019). Inoculation of plant growth promoting bacteria from hyperaccumulator facilitated non-host root development and provided promising agents for elevated phytoremediation efficiency. Chemosphere, 234: 769–776

[52] Wang Q, Xu S A, Wen Z Y, Liu Q Z, Huang L K, Shao G S, Feng Y, Yang X E. (2022a). Combined plant growth-promoting bacteria inoculants were more beneficial than single agents for plant growth and Cd phytoextraction of Brassica juncea L. during field application. Toxics, 10(7): 396

[53] Wang Y, Narayanan M, Shi X J, Chen X P, Li Z L, Natarajan D, Ma Y. (2022b). Plant growth-promoting bacteria in metal-contaminated soil: current perspectives on remediation mechanisms. Frontiers in Microbiology, 13: 966226

[54] Wang Y Y, Yang X E, Zhang X C, Dong L X, Zhang J, Wei Y Y, Feng Y, Lu L L. (2014). Improved plant growth and Zn accumulation in grains of rice (Oryza sativa L.) by inoculation of endophytic microbes isolated from a Zn hyperaccumulator, Sedum alfredii H. Journal of Agricultural and Food Chemistry, 62(8): 1783–1791

[55] Wei S B, Li X, Lu Z F, Zhang H, Ye X Y, Zhou Y J, Li J, Yan Y Y, Pei H C, Duan F Y. . (2022). A transcriptional regulator that boosts grain yields and shortens the growth duration of rice. Science, 377(6604): eabi8455

[56] Wei Z Y, Zhang H Y, Fang M, Lin S Y, Zhu M S, Li Y X, Jiang L M, Cui T L, Cui Y W, Kui H. . (2023). The Dof transcription factor COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation. Molecular Plant, 16(11): 1759–1772

[57] Wu Q B, Pan Y B, Su Y C, Zou W H, Xu F, Sun T T, Grisham M P, Yang S L, Xu L P, Que Y X. (2022). WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane. International Journal of Molecular Sciences, 23(18): 10770

[58] Wu Y J, Ma L Y, Liu Q Z, Vestergård M, Topalovic O, Wang Q, Zhou Q Y, Huang L K, Yang X E, Feng Y. (2020). The plant-growth promoting bacteria promote cadmium uptake by inducing a hormonal crosstalk and lateral root formation in a hyperaccumulator plant Sedum alfredii. Journal of Hazardous Materials, 395: 122661

[59] Wybouw B, Arents H E, Yang B J, Nolf J, Smet W, Vandorpe M, Minne M, Luo X P, De Clercq I, Van Damme D. . (2023). The transcription factor AtMYB12 is part of a feedback loop regulating cell division orientation in the root meristem vasculature. Journal of Experimental Botany, 74(6): 1940–1956

[60] Xie Y, Li X N, Huang X B, Han S J, Amombo E, Wassie M, Chen L, Fu J M. (2019). Characterization of the Cd-resistant fungus Aspergillus aculeatus and its potential for increasing the antioxidant activity and photosynthetic efficiency of rice. Ecotoxicology and Environmental Safety, 171: 373–381

[61] Yang X E, Li T Q, Long X X, Xiong Y H, He Z L, Stoffella P J. (2006). Dynamics of zinc uptake and accumulation in the hyperaccumulating and non-hyperaccumulating ecotypes of Sedum alfredii Hance. Plant and Soil, 284(1−2): 109–119

[62] Yang X E, Long X X, Ye H B, He Z L, Calvert D V, Stoffella P J. (2004). Cadmium tolerance and hyperaccumulation in a new Zn-hyperaccumulating plant species (Sedum alfredii Hance). Plant and Soil, 259(1−2): 181–189

[63] Yao Y J, Xiong E H, Qu X L, Li J F, Liu H L, Quan L P, Lu W Y, Zhu X L, Chen M L, Li K. . (2023). WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean. BMC Genomics, 24(1): 494

[64] You L X, Zhang R R, Dai J X, Lin Z T, Li Y P, Herzberg M, Zhang J L, Al-Wathnani H, Zhang C K, Feng R W. . (2021). Potential of cadmium resistant Burkholderia contaminans strain ZCC in promoting growth of soy beans in the presence of cadmium. Ecotoxicology and Environmental Safety, 211: 111914

[65] Zhang H H, Li X, Xu Z S, Wang Y, Teng Z Y, An M J, Zhang Y H, Zhu W X, Xu N, Sun G Y. (2020). Toxic effects of heavy metals Pb and Cd on mulberry (Morus alba L.) seedling leaves: photosynthetic function and reactive oxygen species (ROS) metabolism responses. Ecotoxicology and Environmental Safety, 195: 110469

[66] Zhao D, Wang P, Zhao F J. (2024). Toxic metals and metalloids in food: current status, health risks, and mitigation strategies. Current Environmental Health Reports, 11(4): 468–483

[67] Zulfiqar U, Jiang W T, Wang X K, Hussain S, Ahmad M, Maqsood M F, Ali N, Ishfaq M, Kaleem M, Haider F U. . (2022). Cadmium phytotoxicity, tolerance, and advanced remediation approaches in agricultural soils; a comprehensive review. Frontiers in Plant Science, 13: 773815

[68] Zuo G Q, Aiken R M, Feng N J, Zheng D F, Zhao H D, Avenson T J, Lin X M. (2022). Fresh perspectives on an established technique: pulsed amplitude modulation chlorophyll a fluore-scence. Plant-Environment Interactions, 3(2): 41–59

RIGHTS & PERMISSIONS

Higher Education Press 2025