Microbial Diversity and Unique Soil-Microbe Interactions Across Western Saudi Arabian Arid Environments

Main Article Content

Wafa A. Alshehri

Abstract

This study investigates microbial diversity in arid soils across Western Saudi Arabia using 16S rRNA analysis. Soil samples were collected from various locations in the Makkah region, with pH levels ranging from 7.00 in Kamil to 7.81 in Khulais. Moisture content varied significantly, from 0.5% in Fair Capital to 12.0% in Jeddah. The sand was identified as the dominant soil component, with varying proportions of silt and clay, classifying all samples as sandy soil. Bacterial incidence showed notable variation, peaking at 20% in Fair Capital and reaching a minimum of 6% in Al-Qunfudhah. Soil composition influenced particle aggregation, with higher clay and moisture content promoting clumping in areas like Jeddah, while lower percentages resulted in loose, scattered particles elsewhere. 16S rRNA sequences from bacterial isolates were matched with similar isolates from the gene bank database. Results reveal diverse microbial communities across the studied region, correlating with varying soil physicochemical properties. This research contributes to our understanding of soil-microbe interactions in arid environments and may inform future soil management strategies in similar ecosystems.

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References

[1] Berg G, Rybakova D, Fischer D (2020). Microbiome definition re-visited: old concepts and new challenges. Microbiome 8 (103): 1-22. https://doi.org/10.1186/s40168-020-00875-0

[2] Abd-ElGawad AM, Assaeed AM, Al-Rowaily SL, Dar BM, Malik JA (2021). Moisture and Salinity Drive the Vegetation Composition of Wadi Hargan, Riyadh, Saudi Arabia. Diversity 13 (11): 587. https://doi.org/10.3390/d13110587

[3] Abdella B, Abozahra NA, Shokrak NM, Mohamed RA, El-Helow ER (2023). Whole spectrum of Aeromonas hydrophila virulence determinants and the identification of novel SNPs using comparative pathogenomics. Sci Rep 13 (1): 7712. doi: 10.1038/s41598-023-34887-1

[4] Al-Hanawi MK, Keetile M (2021). Socio-Economic and Demographic Correlates of Non-communicable Disease Risk Factors Among Adults in Saudi Arabia. Front Med (Lausanne) 8:605912. https://doi: 10.3389/fmed.2021.605912.

[5] Alharbi NM, Alharthi AK, Almihmadi RA, Alaidaroos BA, (2021). Screening and Characterization of Soil Microbes Producing Antimicrobial Compounds in Makkah Province, Saudi Arabia. Biosci. Biotechnol. Res. Asia (18): 719–732. http://dx.doi.org/10.13005/bbra/2954

[6] Al-Obaid S, Samraoui B, Thomas J, El-Serehy HA, Alfarhan AH, Schneider W, O'Connell M (2017). An overview of wetlands of Saudi Arabia: Values, threats, and perspectives. Ambio. 46 (1): 98-108. https://doi: 10.1007/s13280-016-0807-4.

[7] Al-Yamani MN, Al-Sadiq AR (2006). Heavy Metals and Microbial Analysis of Soil Samples Collected From Aramco Gulf Operations Company Al-khafji, (AGOC) Saudi Arabia. Saudi Journal of Biological Sciences (13): no. 2, pp.129-132.

[8] Alzahrani KJ (2021). Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions. Microorganisms 9 (10): 2021. https://doi: 10.3390/microorganisms9102021

[9] Amasha RH (2018). Microbial diversity and phylogenetic studies of some microbes obtained from unexplored caves of Saudi Arabia. J. of Experimental Biology and Agri Sciences 6 (2): 342-351. http://doi: 10.18006/2018.6(2).342.351

[10] APHA (2002). Standard Methods for the Examination of Water and Wastewater. 20th Edition, American Public Health Association. Baltimore, Maryland, U. Standard Methods for the Examination of Water and Wastewater. vol. 6 (American Public Health Association., 1926).

[11] Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006). The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol (57): 233-66. https://doi: 10.1146/annurev.arplant.57.032905.105159

[12] Brevik EC, Steffan JJ, Rodrigo-Comino J, Neubert D, Burgess LC, Cerdà A, (2019). Connecting the public with soil to improve human health. Eur. J. Soil Sci (70): 898–910. https://doi.org/10.1111/ejss.12764

[13] Carter MR, Gregorich EG, (2007). Soil Sampling and Methods of Analysis. Taylor & Francis eBooks ISBN 9780429126222. 1264. https://doi.org/10.1201/9781420005271

[14] Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe SG (2016). Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol (209): 798–811. https://doi.org/10.1111/nph.13697

[15] Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL (2020). Emerging Priorities for Microbiome Research. Front. Microbiol 11:136. https://doi: 10.3389/fmicb.2020.00136

[16] 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. doi: 10.1371/journal.pone.0208223

[17] Escobar-Zepeda A, Godoy-Lozano EE, Raggi L, Segovia L, Merino E, Gutiérrez-Rios RM, Juarez K, Licea-Navarro AF, Pardo-Lopez L, Sanchez-Flores A (2020). Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics. Sci Rep. 10 (1): 4259. https://doi: 10.1038/s41598-020-61219-4.

[18] Faúndez-Urbina CA, Faúndez Urbina CA, Alanís DC, Ramírez E, Seguel O,. Fustos IJ, Donoso PD, de Miranda JH, Rakonjac N, Palma SE, Galleguillos M (2023). Estimating soil water content in a thorny forest ecosystem by time-lapse electrical resistivity tomography (ERT) and HYDRUS 2D/3D simulations. Hydrological Processes 37( 10): e15002. https://doi.org/10.1002/hyp.15002

[19] Fernández-No IC, Böhme K, Caamaño-Antelo S, Barros-Velázquez J, Calo-Mata P (2015). Identification of single nucleotide polymorphisms (SNPs) in the 16S rRNA gene of foodborne Bacillus spp. Food Microbiol. (46): 239–245. https://doi.org/10.1016/j.fm.2014.08.010

[20] Gaulke CA, Sharpton TJ (2018). The influence of ethnicity and geography on human gut microbiome composition. Nat Med (10): 1495-1496. https://doi: 10.1038/s41591-018-0210-8.

[21] Hasanean H, Almazroui M (2015). Rainfall: features and variations over Saudi Arabia, a review. Climate (3): 578-626; https://doi.org/10.3390/cli3030578

[22] Herzallah HK, Antonisamy BR, Shafee MH, Al-Otaibi ST (2019). Temporal trends in the incidence and demographics of cancers, communicable diseases, and non-communicable diseases in Saudi Arabia over the last decade. Saudi Med. J. 40 (3): 277–286. https://doi: 10.15537/smj.2019.3.23585

[23] Jackson M (1967). Soil Chemical Analysis. Prentice-Hall of India Pvt. Ltd., New Delhi, 498p.

[24] Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28 (12): 1647-9. https://doi: 10.1093/bioinformatics/bts199.

[25] Krásný L, Gourse RL (2004). An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J 23 (22): 4473-83. https://doi: 10.1038/sj.emboj.7600423

[26] Krishnan P, Kruger NJ, Ratcliffe RG (2005). Metabolite fingerprinting and profiling in plants using NMR. J Exp Bot 56 (410): 255-65. https://doi: 10.1093/jxb/eri010

[27] Lee KC, Caruso T, Archer SDJ, Gillman LN, Lau MCY, Cary SC, Lee CK, Pointing SB (2018). Stochastic and Deterministic Effects of a Moisture Gradient on Soil Microbial Communities in the McMurdo Dry Valleys of Antarctica. Front Microbiol 1 (9): 2619. https://doi: 10.3389/fmicb.2018.02619

[28] Li T, Liang J, Chen X, Wang H, Zhang S, Pu Y, Xu X, Li H, Xu J, Wu X, Liu X, (2021). The interacting roles and relative importance of climate, topography, soil properties and mineralogical composition on soil potassium variations at a national scale in China. Catena (196): 104875. https://doi.org/10.1016/j.catena.2020.104875

[29] Logan NA, Vos PD (2015). Bacillus. in Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc., in association with Bergey’s Manual Trust. 1–163. https://doi.org/10.1002/9781118960608.gbm00530.

[30] Ma L, Wang H, Wu J, Wang Y, Zhang D, Liu X( 2019). Metatranscriptomics reveals microbial adaptation and resistance to extreme environment coupling with bioleaching performance. Bioresour Technol. (280): 9-17. doi: 10.1016/j.biortech.2019.01.117.

[31] Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA (2015). Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev 39 (2): 203-21. https://doi: 10.1093/femsre/fuu011

[32] Matus FJ (2021). Fine silt and clay content is the main factor defining maximal C and N accumulations in soils: a meta-analysis. Sci Rep. 2021 Mar 19;11(1):6438. https://doi: 10.1038/s41598-021-84821-6

[33] Nanamiya H, Kasai K, Nozawa A, Yun CS, Narisawa T, Murakami K, Natori Y, Kawamura F, Tozawa Y (2008). Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis. Mol Microbiol 67 (2): 291-304. https://doi: 10.1111/j.1365-2958.2007.06018.x.

[34] Neffar S, Chenchouni H, Si Bachir, A (2016). Floristic composition and analysis of spontaneous vegetation of Sabkha Djendli in North-east Algeria. Plant Biosyst. Int. J. Deal. with All Asp. Plant Biol. (150): 396–403. https://doi:10.1080/11263504.2013.810181

[35] Norussis MJ (2006). Statistical Package for Social Science (SPSS) for windows advanced statistics release 15.0. Chicago SPSS.

[36] O’Kelly, B. C. (2004). Accurate Determination of Moisture Content of Organic Soils Using the Oven Drying Method. Drying Technology 22 (7): 1767–1776. https://doi.org/10.1081/DRT-200025642

[37] Premaraj TS, Vella R, Chung J, Lin Q, Hunter P, Underwood K, Premaraj S, Zhou Y (2020). Ethnic variation of oral microbiota in children. Sci Rep 10 (1): 14788. doi: 10.1038/s41598-020-71422-y.

[38] Roumpeka DD, Wallace RJ, Escalettes F, Fotheringham I, Watson M (2017). A review of bioinformatics tools for bio-prospecting from metagenomic sequence data. Front. Genet 8:23. https://doi.org/10.3389/fgene.2017.00023

[39] Ruiz-García C, Quesada E, Martínez-Checa F, Llamas I, Urdaci MC, Béjar V (2005). Bacillus axarquiensis sp. nov. and Bacillus malacitensis sp. nov., isolated from river-mouth sediments in southern Spain. Int J Syst Evol Microbiol 55 (3):1279-1285. https://doi: 10.1099/ijs.0.63567-0

[40] Skariah S, Abdul-Majid S, Hay AG, Acharya A, Kano N, Al-Ishaq RK, de Figueiredo P, Han A, Guzman A, Dargham SR, Sameer S, Kim GE, Khan S, Pillai P, Sultan AA (2023). . Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils. Microbiol Spectr 11 (2): e0346222. https://doi: 10.1128/spectrum.03462-22

[41] Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings Rd, Hengartner NW, Xie G (2013). Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Front Microbiol (29): 4:84. https://doi: 10.3389/fmicb.2013.00084

[42] Voltr V, Menšík L, Hlisnikovský L, Hruška M, Pokorný E, Pospíšilová L (2021). The Soil Organic Matter in Connection with Soil Properties and Soil Inputs. Agronomy 11 (4): 779. https://doi.org/10.3390/agronomy11040779

[43] Waksman SA (1922). A Method for Counting the Number of Fungi in the Soil. J Bacteriol. 1922 May;7(3):339-41. https://doi: 10.1128/jb.7.3.339-341.1922.

[44] Wang LT, Lee FL, Tai CJ, Yokota A, Kuo HP (2007). Reclassification of Bacillus axarquiensis Ruiz-Garcia et al. 2005 and Bacillus malacitensis Ruiz-Garcia et al. 2005 as later heterotypic synonyms of Bacillus mojavensis Roberts et al. 1994. Int J Syst Evol Microbiol 57 (7): 1663-1667. https://doi: 10.1099/ijs.0.64808-0

[45] Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L (2009). Impact of genome reduction on bacterial metabolism and its regulation. Science 326 (5957): 1263-8. https://doi: 10.1126/science.1177263

[46] Zhang S, Haldenwang WG (2003). RelA is a component of the nutritional stress activation pathway of the Bacillus subtilis transcription factor sigma B. J Bacteriol 185 (19): 5714-21. https://doi: 10.1128/JB.185.19.5714-5721.2003