About the Journal
In Memory of Professor Jerzy Radecki
Ownership and Management Statement
Editorial Office
Editorial Board
Scope
Impact Factor
Indexed by
Journal Impact Factor contributing items
Publication Frequency
Revenue Sources & Business Model
Contact
Subscription
Current issue
Online first
Instructions for Authors
Copyright & Licensing
Publication Fees
Editorial policies
Publication Policy Overview
Peer Review Policy
Research Ethics and Malpractice Policy
Plagiarism Policy
Conflict of Interest Policy
Open Access Policy
Instructions for Reviewers
Generative AI and AI-Assisted Technologies Policy
Advertising Policy
Direct Marketing & Manuscript Solicitation
Digital Archiving and Preservation Policy
CrossMark, Correction, and Retraction Policy
Archive
Publication Fees
Copyright & Licensing
Editorial policies
Publication Policy Overview
Peer Review Policy
Research Ethics and Malpractice Policy
Plagiarism Policy
Conflict of Interest Policy
Open Access Policy
Instructions for Reviewers
Generative AI and AI-Assisted Technologies Policy
Advertising Policy
Direct Marketing & Manuscript Solicitation
Digital Archiving and Preservation Policy
CrossMark, Correction, and Retraction Policy
eISSN: 2083-5906
ISSN: 1230-1485
ISSN: 1230-1485
ORIGINAL RESEARCH
Investigating Mutational Robustness of 16S
Ribosomal RNA in Bacteria
from Saudi Arabia Soil
1
Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 23890, Saudi Arabia
Submission date: 2024-05-04
Final revision date: 2024-07-17
Acceptance date: 2024-08-15
Online publication date: 2024-12-30
Publication date: 2025-08-20
Corresponding author
Wafa A. Alshehri
Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 23890, Saudi Arabia
Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 23890, Saudi Arabia
Pol. J. Environ. Stud. 2025;34(5):6049-6067
KEYWORDS
TOPICS
ABSTRACT
A study was conducted on 16S rRNA sequences for Klebsiella aerogenes, K. pneumoniae,
and Proteus mirabilis strains from Saudi soil to investigate the genetic variations among them.
The analysis revealed minimal differences among these strains. Single nucleotide polymorphisms (SNPs)
were identified in the 16S rRNA genes of K. aerogenes and K. pneumoniae strains, indicating genetic
diversity within these bacterial populations that could potentially influence their phenotypic traits.
Additionally, the presence of insertions and deletions (indels) in comparison to separate rRNA gene
sequences suggested structural variations in the genetic makeup of these strains. Electropherograms
displayed multiple peaks at specific nucleotide positions, indicating the presence of different nucleotides
within the gene copies. This suggests the existence of genetic heterogeneity within the populations,
possibly due to the coexistence of multiple variants of the 16S rRNA gene within individual bacterial
strains. Overall, there are valuable insights into the genetic variations and relationships among these
bacterial strains found in Saudi soil. Understanding the genetic diversity of these bacterial strains
is crucial for comprehending evolutionary relationships and potential differences in phenotypic
characteristics. The results contribute to the knowledge about the genetic variation of bacteria in soil
in Saudi Arabia, with potential implications for environmental microbiology and biotechnology.
CONFLICT OF INTEREST
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
REFERENCES (49)
1.
PETIBON C., GHULAM M.M., CATALA M., ABOU ELELA S. Regulation of ribosomal protein genes: An ordered anarchy. WIREs RNA, 12, e1632, 2021. https://doi.org/10.1002/wrna.1....
2.
KUSHWAHA A.K., BHUSHAN S. Unique structural features of the Mycobacterium ribosome. Progress in Biophysical Molecular Biology, 152, 15, 2020. https://doi.org/10.1016/j.pbio....
3.
ASEEV L.V., KOLEDINSKAYA L.S., BONI I.V. Extraribosomal Functions of Bacterial Ribosomal Proteins - An Update, 2023. International Journal of Molecular Sciences, 25 (5), 2957, 2024. https://doi.org/10.3390/ijms25....
4.
JOHNSON J.S., SPAKOWICZ D.J., HONG BY., PETERSEN, L.M., DEMKOWICZ P., CHEN L., LEOPOLD S.R., HANSON B.M., AGRESTA H.O., GERSTEIN M., SODERGREN E., WEINSTOCK G.M. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications, 10, 5029, 2019. https://doi.org/10.1038/s41467....
5.
SANTOS A., VAN AERLE R., BARRIENTOS L., MARTINEZ-URTAZA J. Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Computional Structure Biotechnology Journal, 18, 296, 2020. https://doi.org/10.1016/j.csbj....
6.
THEISSINGER K., FERNANDES C., FORMENTI G., BISTA I., BERG P.R., BLEIDORN C., BOMBARELY A., CROTTINI A., GALLO G.R., GODOY J.A., JENTOFT S., MALUKIEWICZ J., MOUTON A., OOMEN R.A., PAEZ S., PALSBØLL P.J., PAMPOULIE C., RUIZ-LÓPEZ M.J., SECOMANDI S., SVARDAL H., THEOFANOPOULOU C., DE VRIES J., WALDVOGEL A.-M., ZHANG G., JARVIS E.D., BÁLINT M., CIOFI C., WATERHOUSE R.M., MAZZONI C.J., HÖGLUND J. How genomics can help biodiversity conservation. Trends in Genetics, 39 (7), 545, 2023.
7.
WOO P.C.Y., LAU S.K.P., TENG J.L.L., TSE H., YUEN K.-Y. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clinical Microbiology Infection, 14 (10), 908, 2008. https://doi.org/10.1111/j.1469....
8.
LUDWIG W., KLENK H.-P. Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's manual Systematic Bacteriology; Brenner D.J., Krieg N.R., Staley J.T., Garrity G.M. (eds), Springer, Boston, MA, pp. 49, 2005. https://doi.org/10.1007/0-387-....
9.
LEEWIS M.-C., LAWRENCE C.R., SCHULZ M.S., TFAILY M.M., AYALA-ORTIZ C.O., FLORES G.E., MACKELPRANG R., MCFARLAND J.W. The influence of soil development on the depth distribution and structure of soil microbial communities. Soil Biology and Biochemistry, 174, 108808, 2022. https://doi.org/10.1016/j.soil....
10.
COLE J.R., WANG Q., CARDENAS E., FISH J., CHAI B., FARRIS R.J., KULAM-SYED-MOHIDEEN A.S., MCGARRELL D.M., MARSH T., GARRITY G.M., TIEDJE J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research, 37, D141, 2009. https://doi.org/10.1093/nar/gk....
11.
ALTSCHUL S.F., MADDEN T.L., SCHÄFFER A.A., ZHANG J., ZHANG Z., MILLER W., LIPMAN D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25 (17), 3389, 1997. https://doi.org/10.1093/nar/25....
12.
HALL T.A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95, 1999.
13.
McWILLIAM H., LI W., ULUDAG M., SQUIZZATO S., PARK Y.M., BUSO N., COWLEY A.P., LOPEZ R. Analysis tool web services from the EMBL-EBI. Nucleic Acids Research, 41(Web Server issue), W597, 2013. https://doi.org/10.1093/nar/gk....
14.
CASTRESANA J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17 (4), 540, 2000. https://doi.org/10.1093/oxford....
15.
TALAVERA G., CASTRESANA J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56, 564, 2007. https://doi.org/10.1080/106351....
16.
KUMAR P., KUSCU C., DUTTA A. Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Trends in Biochemical Sciences, 41 (8), 679, 2016. https://doi.org/10.1016/j.tibs....
17.
CANNONE J.J., SUBRAMANIAN S., SCHNARE M.N., COLLETT J.R., D'SOUZA L.M., DU Y., FENG B., LIN N., MADABUSI L.V., MÜLLER K.M., PANDE N., SHANG Z., YU N., GUTELL R.R. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 1, 2002. https://doi.org/10.1186/1471-2....
18.
OLSON W.K., LI S., KAUKONEN T., COLASANTI A.V., XIN Y., LU X.J. Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs. Biochemistry, 58 (20), 2474, 2019. https://doi.org/10.1021/acs.bi....
19.
MEDINA-CHÁVEZ N.O., TRAVISANO M. Archaeal Communities: The Microbial Phylogenomic Frontier. Frontier Journal of Genetics, 12, 693193, 2022. https://doi.org/10.3389/fgene.....
20.
PANTHEE B., GYAWALI S., PANTHEE P., TECHATO K. Environmental and human microbiome for health. Life, 12, 456, 2022. https://doi.org/10.3390/life12....
21.
RAPPUOLI R., YOUNG P., RON E. PECETTA S., PIZZA M. Save the microbes to save the planet. A call to action of the International Union of the Microbiological Societies (IUMS). One Health Outlook, 5, 5, 2023. https://doi.org/10.1186/s42522....
22.
DRANCOURT M., BOLLET C., CARLIOZ A., MARTELIN R., GAYRAL J.-P., RAOULT D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. Journal of Clinical Microbiology, 38 (10), 3623, 2000. https://doi.org/10.1128/JCM.38....
23.
HAKOVIRTA J.R., PREZIOSO S., HODGE D., PILLAI S.P., WEIGEL L.M. Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group. Journal of Clinical Microbiology, 54 (11), 2749, 2016. https://doi.org/10.1128/JCM.01....
24.
CLARK D.P., PAZDERNIK N.J., MCGEHEE M.R. Regulation of Transcription in Prokaryotes. In: Molecular Biology, 3rd ed.; Clark D.P., Pazdernik N.J., McGehee M.R., Elsevier B.V., pp. 522-559, 2019. https://doi.org/10.1016/B978-0....
25.
NAJJARI A., STATHOPOULOU P., ELMNASRI K., HASNAOUI F., ZIDI I., SGHAIER H., OUZARI H.I., CHERIF A., TSIAMIS G. Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia. Biology (Basel), 10 (5), 397, 2021. https://doi.org/10.3390/biolog....
26.
GREENBLUM S., CARR R., BORENSTEIN E. Extensive strain-level copy-number variation across human gut microbiome species. Cell, 160, 583, 2015. https://doi.org/10.1016/j.cell....
27.
SHAIKH F.Y., WHITE J.R., GILLS J.J., HAKOZAKI T., RICHARD C., ROUTY B., OKUMA Y., USYK M., PANDEY A., WEBER J.S., AHN J., LIPSON E.J., NAIDOO J., PARDOLL D.M., SEARS C.L. A uniform computational approach improved on existing pipelines to reveal microbiome biomarkers of nonresponse to immune checkpoint inhibitors. Clinical Cancer Research, 27 (9), 2571, 2021. https://doi.org/10.1158/1078-0....
28.
KONER S., CHEN J.-S., HSU B.-M., TAN C.-W., FAN C.-W., CHEN T.-H., HUSSAIN B., NAGARAJAN V. Assessment of carbon substrate catabolism pattern and functional metabolic pathway for microbiota of limestone caves. Microorganisms, 9 (8), 1789, 2021. https://doi.org/10.3390/microo....
29.
CHECCUCCI A., LUISE D., MODESTO M., CORREA F., BOSI P., MATTARELLI P., TREVISI P. Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota. Applied Microbiology and Biotechnology, 105 (14-15), 6033, 2021. https://doi.org/10.1007/s00253....
30.
SPRING S., SCHEUNER C., GÖKER M., KLENK H.P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology, 6, 1, 2015. https://doi.org/10.3389/fmicb.....
31.
HASSLER H.B., PROBERT B., MOORE C., LAWSON E., JACKSON R.W., RUSSELL B.T., RICHARDS V.P. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. Microbiome, 10, 104, 2022. https://doi.org/10.1186/s40168....
32.
LONG S.W., LINSON S.E., OJEDA SAAVEDRA M., CANTU C., DAVIS J.J., BRETTIN T., OLSEN R.J. Whole-Genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere, 2 (4), e00290, 2017. https://doi.org/10.1128/mSpher....
33.
ROCHA J., HENRIQUES I, GOMILA M, MANAIA CM. Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings. Scientific Reports, 12 (1), 10441, 2022. https://doi.org/10.1038/s41598....
34.
JANDA J.M., ABBOTT S.L. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Journal of Clinical Microbiology, 45 (9), 2761, 2007. https://doi.org/10.1128/JCM.01....
35.
MARTIN R.M., BACHMAN M.A. Colonization, Infection, and the Accessory Genome of Klebsiella pneumoniae. Frontiers in Cell Infection Microbiology, 8, 4, 2018. https://doi.org/10.3389/fcimb.....
36.
BARTOŠ O., CHMEL M., SWIERCZKOVÁ I. The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification. Scientific Reports, 14 (1), 9067, 2024. https://doi.org/10.1038/s41598....
37.
KARIMI E., KELLER-COSTA, T., SLABY B.M., COX C.J., da ROCHA U.N., HENTSCHEL U., COSTA R. Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Scientific Reports, 9, 1999, 2019. https://doi.org/10.1038/s41598....
38.
CASTELLE1 C.J., BANFIELD J.F. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell, 172, 1181, 2018. https://doi.org/10.1016/j.cell....
39.
FERNANDES M.L.P., BASTIDA F., JEHMLICH N., MARTINOVIĆ T., VĚTROVSKÝ T., BALDRIAN P., DELGADO-BAQUERIZO M., STARKE R. Functional soil mycobiome across ecosystems. Journal of Proteomics, 252, 104428, 2022. https://doi.org/10.1016/j.jpro....
40.
HROVAT K., DUTILH B.E., MEDEMA M.H., MELKONIAN C. Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria, ISME Communications, 4 (1), ycae034, 2024. https://doi.org/10.1093/ismeco....
41.
BOSE N., MOORE S.D. Variable Region Sequences Influence 16S rRNA Performance. Microbiology Spectrum, 11 (3), e0125223, 2023. https://doi.org/10.1128/spectr....
42.
EVANS G.W., CRAGGS T., KAPANIDIS A.N. The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. Journal of Molecular Biology, 434 (2), 167410, 2022. https://doi.org/10.1016/j.jmb.....
43.
FOSTER-NYARKO E., PALLEN M.J. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiology Review, 46 (3), fuac008, 2022. https://doi.org/10.1093/femsre....
44.
QUINN T.P., ERB I., RICHARDSON M.F., CROWLEY T.M. Understanding sequencing data as compositions: an outlook and review. Bioinformatics, 34 (16), 2870, 2018. https://doi.org/10.1093/bioinf....
45.
CAUDILL M.T., BRAYTON K.A. The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples. Microorganisms, 10 (3), 605, 2022. https://doi.org/10.3390/microo....
46.
MANSILLA C.A. DOMÍNGUEZ E., MACKENZIE R., HOYOS-SANTILLAN J., HENRÍQUEZ M.J., ARAVENA J.C., VILLA-MARTÍNEZ R. Peatlands in Chilean Patagonia: Distribution, Biodiversity, Ecosystem Services, and Conservation. In: Conservation in Chilean Patagonia. Integrated Science, Castilla J.C., Armesto Zamudio J.J., Martínez-Harms M.J., Tecklin D. (eds), 19. Springer, Cham, pp. 153-174, 2024. https://doi.org/10.1007/978-3-....
47.
VERBEKE B.A., LAMIT L.J., LILLESKOV E.A., HODGKINS S.B., BASILIKO N., KANE E.S., ANDERSEN R., ARTZ R.R.E., BENAVIDES J.C., BENSCOTER B.W., BORKEN W., BRAGAZZA L., BRANDT S.M., BRÄUER S.L., CARSON M.A., CHARMAN D., CHEN X., CLARKSON B.R., COBB A.R., CONVEY P., DEL ÁGUILA PASQUEL J., ENRIQUEZ A.S., GRIFFITHS H., GROVER S.P., HARVEY C.F., HARRIS L.I., HAZARD C., HODGSON D., HOYT A.M., HRIBLJAN J., JAUHIAINEN J., JUUTINEN S., KNORR K.H., KOLKA R.K., KÖNÖNEN M., LARMOLA T., MCCALLEY C.K., MCLAUGHLIN J., MOORE T.R., MYKYTCHUK N., NORMAND A.E., RICH V., ROULET N., ROYLES J., RUTHERFORD J., SMITH D.S., SVENNING M.M., TEDERSOO L., THU P.Q., TRETTIN C.C., TUITTILA E.S., URBANOVÁ Z., VARNER R.K., WANG M., WANG Z., WARREN M., WIEDERMANN M.M., WILLIAMS S., YAVITT J.B., YU Z.G., YU Z., CHANTON J.P. Latitude, elevation, and mean annual temperature predict peat organic matter chemistry at a global scale. Global Biogeochemical Cycles, 36, e2021GB007057, 2022. https://doi.org/10.1029/2021GB....
48.
IBAL J.C., PHAM H.Q., PARK C.E., SHIN J.-H. Information about variations in multiple copies of bacterial 16S rRNA genes may aid in species identification. PLoS One, 14, e0212090, 2019. https://doi.org/10.1371/journa....
49.
DA SILVA C.B., DOS SANTOS H.R.M., MARBACH P.A.S., DE SOUZA J.T., CRUZ-MAGALHÃES V., ARGÔLO-FILHO R.C., LOGUERCIO L.L. First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds. PeerJ, 7, e7452, 2019. https://doi.org/10.7717/peerj.....
Share
RELATED ARTICLE
| eISSN: | 2083-5906 |
| ISSN: | 1230-1485 |
We process personal data collected when visiting the website. The function of obtaining information about users and their behavior is carried out by voluntarily entered information in forms and saving cookies in end devices. Data, including cookies, are used to provide services, improve the user experience and to analyze the traffic in accordance with the Privacy policy. Data are also collected and processed by Google Analytics tool (more).
You can change cookies settings in your browser. Restricted use of cookies in the browser configuration may affect some functionalities of the website.
You can change cookies settings in your browser. Restricted use of cookies in the browser configuration may affect some functionalities of the website.
