Investigating the metagenomics of the bacterial communities in the rhizosphere of the desert plant Senna italica and their role as plant growth promoting factors


  • Asrar M. ALSWAT University of Jeddah, College of Science, Department of Biology, Jeddah 21493 (SA)
  • Rewaa S. JALAL University of Jeddah, College of Science, Department of Biology, Jeddah 21493 (SA)
  • Ashwag Y. SHAMI Princess Nourah bint Abdulrahman University, College of Sciences, Department of Biology, P.O. Box 84428, Riyadh 11671 (SA)
  • Mazen A. MAJEED University of Jeddah, College of Science, Department of Biology, Jeddah 21493 (SA)
  • Zohoor S. ALSAEDI University of Jeddah, College of Science, Department of Biology, Jeddah 21493 (SA)
  • Lina BAZ King Abdulaziz University, Faculty of Science, Department of Biochemistry, Jeddah 21589 (SA)
  • Mohammed Y. REFAI University of Jeddah, College of Science, Department of Biochemistry, Jeddah 21493 (SA)
  • Mohammed N. BAESHEN University of Jeddah, College of Science, Department of Biology, Jeddah 21493 (SA)
  • Noor M. BATAWEEL King Fahad Medical Research Center, P.O. Box 80216, King Abdulaziz University, Jeddah, 21589 (SA)
  • Ahmed AL-HEJIN King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Jeddah (SA)
  • Ruba A. ASHY University of Jeddah, College of Science, Department of Biology, Jeddah 21493 (SA)



metagenomics, microbiome, PGPR, rhizosphere, Senna italica plant


Natural microbial communities associated with desert plants are found in soils that face nutrient deficiencies and extreme environments, including salinity and drought. In this study, 16S rRNA metagenomic sequencing was used to screen and identify bacterial assemblies associated with the desert plant Senna italica, obtained from diverse soil samples located in the Asfan region, northeast of Jeddah, Saudi Arabia. Several studies found Senna italica as a valuable medicinal plant for treating different diseases; however, a few studies were done on its association with bacterial communities under drought conditions. This study aimed to identify bacterial communities present in the drought soil environment of the Senna italica plants. To approach our goals, we applied metagenomic techniques, discovering a new bacterial strain beneficial for biotechnological applications. Our results showed that the analysis of the 16S rRNA sequences at the taxonomic phylum level detected 15 phyla of bacterial populations in the soil samples. The most prevalent was kept for further research. Our findings demonstrated that rhizospheric bacteria may be used as indicators of plant growth rate and survival ability in hostile environments. Studying the soil microbiome's taxonomic, phylogenetic, and functional diversity will facilitate identifying new candidates for biological agents that can be used to improve agricultural and industrial processes.


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Adjou ES, Koudoro AY, Nonviho G (2021). Phytochemical profile and potential pharmacological properties of leaves extract of Senna italica Mill. American Journal of Pharmacological Sciences 9(1):36-39.

Alsaedi ZS, Ashy RA, Shami AY, Majeed MA, Alswat AM, Baz L, ... Jalal RS (2022). Metagenomic study of the communities of bacterial endophytes in the desert plant Senna italica and their role in abiotic stress resistance in the plant. Brazilian Journal of Biology 82.

Alves LDF, Westmann CA, Lovate GL, de Siqueira GMV, Borelli TC, Guazzaroni ME (2018). Metagenomic approaches for understanding new concepts in microbial science. International Journal of Genomics.

Aslam MM, Idris AL, Zhang QIAN, Weifeng XU, Karanja JK, Wei YUAN (2022). Rhizosphere microbiomes can regulate plant drought tolerance. Pedosphere 32(1):61-74.

Baeshen MN, Moussa TAA, Ahmed F, Abulfaraj AA, Jalal RS, Majeed MA, ... Huelsenbeck JP (2020). Diversity Profiling of associated bacteria from the soils of stress tolerant plants from seacoast of Jeddah, Saudi Arabia. Applied Ecology and Environmental Research 18(6):8217-8231.

Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk HP, ... van Wezel GP (2016). Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews 80(1):1-43.

Battisti DS, Naylor RL (2009). Historical warnings of future food insecurity with unprecedented seasonal heat. Science 323(5911):240-244.

Berendsen RL, Pieterse CMJ, Bakker PAHM (2012). The rhizosphere microbiome and plant health. Trends in Plant Science 17(8):478-486.

Berg G, Grube M, Schloter M, Smalla K (2014). Unraveling the plant microbiome: looking back and future perspectives. Frontiers in Microbiology 5.

Bodenhausen N, Horton MW, Bergelson J (2013). Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 8(2).

Bonfante P, Anca IA (2009). Plants, mycorrhizal fungi, and bacteria: A network of interactions. Annual Review of Microbiology 63:363-383.

Bouskill NJ, Lim HC, Borglin S, Salve R, Wood TE, Silver WL, Brodie EL (2013). Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. The ISME Journal 7(2):384-394.

Bu X, Gu X, Zhou X, Zhang M, Guo Z, Zhang J, ... Wang X (2018). Extreme drought slightly decreased soil labile organic C and N contents and altered microbial community structure in a subtropical evergreen forest. Forest Ecology and Management 429:18-27.

Bui EN (2013). Soil salinity: A neglected factor in plant ecology and biogeography. Journal of Arid Environments 92(June):14-25.

Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, ... Schulze-Lefert P (2015). Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host & Microbe 17(3):392-403.

Cerri CEP, Sparovek G, Bernoux M, Easterling WE, Melillo JM, Cerri CC (2007). Tropical agriculture and global warming: impacts and mitigation options. Scientia Agricola 64:83-99.

Chao A, Bunge J (2002). Estimating the number of species in a stochastic abundance model. Biometrics 58(3):531-539.

Chaparro JM, Sheflin AM, Manter DK, Vivanco JM (2012). Manipulating the soil microbiome to increase soil health and plant fertility. Biology and Fertility of Soils 48:489-499.

Dabai YU (2012). Phytochemical screening and antibacterial activity of the leaf and root extracts of Senna italica. African Journal of Pharmacy and Pharmacology 6(12).

del Carmen Orozco-Mosqueda M, del Carmen Rocha-Granados M, Glick BR, Santoyo G (2018). Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiological Research 208:25-31.

Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW (2012). Transforming clinical microbiology with bacterial genome sequencing. Nature Reviews Genetics 13(9):601-612.

Eida AA, Ziegler M, Lafi FF, Michell CT, Voolstra CR, Hirt H, Saad MM (2018). Desert plant bacteria reveal host influence and beneficial plant growth properties. PLoS One 13(12):e0208223.

Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, ... Caporaso JG (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences 109(52):21390-21395.

Fu H (2014). Research progress on the Actinomyces arthrobacter. Advances in Microbiology 04(12):747-753.

Functions P (2020). Microorganisms for Sustainability. Rhizosphere microbes.

Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, ... Toulmin C (2010). Food security: the challenge of feeding 9 billion people. Science 327(5967):812-818.

Gornall J, Betts R, Burke E, Clark R, Camp J, Willett K, Wiltshire A (2010). Implications of climate change for agricultural productivity in the early twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 365(1554):2973-2989.

Hernández M, Dumont MG, Yuan Q, Conrad R (2015). Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Applied and Environmental Microbiology 81(6):2244-2253.

Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, Ficke A, ... Nelson EB (2000). Methods for assessing the composition and diversity of soil microbial communities. Applied Soil Ecology 15(1):25-36.

Jang SW, Yoou MH, Hong WJ, Kim YJ, Lee EJ, Jung KH (2020). Re-analysis of 16S amplicon sequencing data reveals soil microbial population shifts in rice fields under drought condition. Rice 13:1-7.

Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL (2020). Recent understanding of soil acidobacteria and their ecological significance: a critical review. Frontiers in Microbiology 11:580024.

Kawo AH (2011). Studies on the antibacterial activity and chemical constituents of Khaya senegalensis and Ximenia americana leaf extracts. African Journal of Microbiology Research 5(26):1-7.

Khan MIR, Fatma M, Per TS, Anjum NA, Khan NA (2015). Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants. Frontiers in Plant Science 6:462.

Kuźniar A, Włodarczyk K, Wolińska A (2019). Agricultural and other biotechnological applications resulting from trophic plant-endophyte interactions. Agronomy 9(12).

Lee JJ, Kang MS, Kim GS, Lee CS, Lim S, Lee J, ... Kim MK (2016). Flavisolibacter tropicus sp. nov., isolated from tropical soil. International Journal of Systematic and Evolutionary Microbiology 66(9):3413-3419.

Lesk C, Rowhani P, Ramankutty N (2016). Influence of extreme weather disasters on global crop production. Nature 529(7584):84-87.

Li J, Gao R, Chen Y, Xue D, Han J, Wang J, ... Zhang W (2020). Isolation and Identification of Microvirga thermotolerans HR1, a novel thermo-tolerant bacterium, and comparative genomics among Microvirga species. Microorganisms 8(1):101.

Macrogen (2017). NGS Analysis Manual – OUT. pp 1-16.

Majeed MA, Baeshen M, Afifi m, Ahmed f. (2020). metagenomics of bacterial communities associated with the halophytic plant. EC Microbiology 16(3):1-11.

Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA (2015). Microbial ecology of hot desert edaphic systems. FEMS Microbiology Reviews 39(2):203-221.

Marasco R, Rolli E, Ettoumi B, Vigani G, Mapelli F, Borin S, ... Daffonchio D (2012). A drought resistance-promoting microbiome is selected by root system under desert farming. PloS One 7(10):e48479.

Mashiane RA, Ezeokoli OT, Adeleke RA, Bezuidenhout CC (2017). Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa. World Journal of Microbiology and Biotechnology 33:1-12.

Mengual C, Schoebitz M, Azcón R, Roldán A (2014). Microbial inoculants and organic amendment improves plant establishment and soil rehabilitation under semiarid conditions. Journal of Environmental Management 134:1-7.

Mittler R (2006). Abiotic stress, the field environment and stress combination. Trends in Plant Science 11(1):15-19.

Morgan JAW, Bending GD, White PJ (2005). Biological costs and benefits to plant-microbe interactions in the rhizosphere. Journal of Experimental Botany 56(417):1729-1739.

Naylor D, Coleman-Derr D (2018). Drought stress and root-associated bacterial communities. Frontiers in Plant Science 8.

Niu B, Paulson JN, Zheng X, Kolter R (2017). Simplified and representative bacterial community of maize roots. Proceedings of the National Academy of Sciences 114(12):E2450-E2459.

Noor SO, Al-Zahrani DA, Hussein RM, Jalal RS, Abulfaraj AA, Majeed MA, ... Huelsenbeck JP (2020). Biodiversity in bacterial phyla composite in arid soils of the community of desert medicinal plant Rhazya stricta. Journal of Pharmaceutical Research International 88-98.

Orsini SS, Lewis AM, Rice KC (2017). Investigation of simulated microgravity effects on streptococcus mutans physiology and global gene expression. Microgravity 3(1):0-1.

Pandey P, Irulappan V, Bagavathiannan MV, Senthil-Kumar M (2017). Impact of combined abiotic and biotic stresses on plant growth and avenues for crop improvement by exploiting physio-morphological traits. Frontiers In Plant Science 8:537.

Serraj R, Pingali P (2019). Agriculture & Food Systems to 2050. World Scientific.

Shailendra Singh GG (2015). Plant Growth Promoting Rhizobacteria (PGPR): Current and future prospects for development of sustainable agriculture. Journal of Microbial & Biochemical Technology 07(02).

Soussi A, Ferjani R, Marasco R, Guesmi A, Cherif H, Rolli E, ... Cherif A (2016). Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential. Plant and Soil 405:357-370.

Steven B, Gallegos-Graves LV, Belnap J, Kuske CR (2013). Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material. FEMS Microbiology Ecology 86(1):101-113.

Theodorakopoulos N, Bachar D, Christen R, Alain K, Chapon V (2013). Exploration of Deinococcus‐Thermus molecular diversity by novel group‐specific PCR primers. Microbiologyopen 2(5):862-872.

Tshikalange TE, Meyer JJM, Hussein AA (2005). Antimicrobial activity, toxicity and the isolation of a bioactive compound from plants used to treat sexually transmitted diseases. Journal of Ethnopharmacology 96(3):515-519.

Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015). The importance of the microbiome of the plant holobiont. New Phytologist 206(4):1196-1206.

Varma A, Tripathi S, Prasad R (no date). Microbiome Paradigm.

Wang R, Zhang H, Sun L, Qi G, Chen S, Zhao X (2017). Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak. Scientific Reports 7(1):1-10.

Wardle DA, Bardgett RD, Klironomos JN, Setala H, Van Der Putten WH, Wall DH (2004). Ecological linkages between aboveground and belowground biota. Science 304(5677):1629-1633.

Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, ... Gilbert JA (2015). The soil microbiome influences grapevine-associated microbiota. MBio 6(2):e02527-14.

Zhang JY, Liu XY, Liu SJ (2009). Adhaeribacter terreus sp. nov., isolated from forest soil. International Journal of Systematic and Evolutionary Microbiology 59(7)L1595-1598.

Zhao Y, Song C, Dong H, Luo Y, Wei Y, Gao J, ... Sheng H (2018). Community structure and distribution of culturable bacteria in soil along an altitudinal gradient of Tianshan Mountains, China. Biotechnology & Biotechnological Equipment 32(2):397-407.



How to Cite

ALSWAT, A. M., JALAL, R. S., SHAMI, A. Y., MAJEED , M. A., ALSAEDI, Z. S., BAZ, L., REFAI, M. Y., BAESHEN, M. N., BATAWEEL, N. M., AL-HEJIN, A., & ASHY , R. A. (2023). Investigating the metagenomics of the bacterial communities in the rhizosphere of the desert plant Senna italica and their role as plant growth promoting factors. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51(1), 13053.



Research Articles
DOI: 10.15835/nbha51113053

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