Skip to main content

Advertisement

SpringerLink
Log in

Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis

  • Microbiology of Aquatic Systems
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Asit KB (1970) History of hydrology. North Holland Publishing Company, Amsterdam

    Google Scholar 

  2. Khatri N, Tyagi S (2015) Influences of natural and anthropogenic factors on surface and groundwater quality in rural and urban areas. Front Life Sci 8(1):23–39

    Article  CAS  Google Scholar 

  3. Fan L, Song C, Meng S, Qiu L, Zheng Y, Wu W, Qu J, Li D, Zhang C, Hu G (2016) Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River. Sci Rep 6:39147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD (2017) Bacterial community composition and dynamics spanning five years in freshwater bog lakes. mSphere 2(3):e00169–e00117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH (2017) Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS One 12(5):e0177488

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ (2015) Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River. Sci Total Environ 505:435–445

    Article  CAS  PubMed  Google Scholar 

  7. Youssef NH, Ashlock-Savage KN, Elshahed MS (2012) Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats. Appl Environ Microbiol 78(5):1332–1344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ali E, Shabaan-Dessouki S, Soliman A, El Shenawy A (2014) Characterization of chemical water quality in the Nile River, Egypt. Int J Pure Appl Biosci 2(3):35–53

    Google Scholar 

  9. Badr E-SA, El-Sonbati MA (1772) Nassef HM (2013) Water quality assessment in the Nile River, Damietta branch, Egypt. Catrina 283:1–23

    Google Scholar 

  10. Sutcliffe J, Hurst S, Awadallah AG, Brown E, Hamed K (2016) Harold Edwin Hurst: the Nile and Egypt, past and future. Hydrol Sci J 61(9):1557–1570

    Article  Google Scholar 

  11. Fielding L, Najman Y, Millar I, Butterworth P, Garzanti E, Vezzoli G, Barfod D, Kneller B (2018) The initiation and evolution of the River Nile. Earth Planet Sci Lett 489:166–178

    Article  CAS  Google Scholar 

  12. Mellander P-E, Gebrehiwot SG, Gärdenäs AI, Bewket W, Bishop K (2013) Summer rains and dry seasons in the Upper Blue Nile Basin: the predictability of half a century of past and future spatiotemporal patterns. PLoS One 8(7):e68461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Abu-Lughod JL, AlSayyad N (2017) Encyclopædia Britannica, inc. Encyclopædia Britannica [Internet]. https://www.britannica.com/place/Cairo. Accessed 1 Jul 2020

  14. El-Sheekh M (2009) River Nile pollutants and their effect on life forms and water quality. In: Dumont HJ (eds) The Nile. Monographiae Biologicae, vol 89. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9726-3_19

  15. El Gohary R (2015) Agriculture, industry, and wastewater in the Nile Delta. IJSRAS 2:159–172

    Article  Google Scholar 

  16. Abdel-Satar AM, Ali MH, Goher ME (2017) Indices of water quality and metal pollution of Nile River, Egypt. Egypt J Aquat Res 43(1):21–29

    Article  Google Scholar 

  17. Rennie HG (2020) Water management in New Zealand's Canterbury Region: a sustainability framework Bryan R. Jenkins. Springer, Dordrecht, 2018, pp 524. N Z Geog 76:162–163. https://doi.org/10.1111/nzg.12272

  18. Eraqi WA, ElRakaiby MT, Megahed SA, Yousef NH, Elshahed MS, Yassin AS (2018) The Nile River microbiome reveals a remarkably stable community between wet and dry seasons, and sampling sites, in a large urban metropolis (Cairo, Egypt). Omics 22(8):553–564

    Article  CAS  PubMed  Google Scholar 

  19. APHA (2005) Standard methods for the examination of water and wastewater. American Public Health Association (APHA), Washington, DC

    Google Scholar 

  20. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6(8):1621–1624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(D1):D590–D596

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270

    Google Scholar 

  24. Chao A, Lee S-M (1992) Estimating the number of classes via sample coverage. J Am Stat Assoc 87(417):210–217

    Article  Google Scholar 

  25. Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423 623--656

    Article  Google Scholar 

  26. Simpson EH (1949) Measurement of diversity. Nature 163(4148):688

    Article  Google Scholar 

  27. Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J (2017) MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res 45(W1):W180–W188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12(6):R60

    Article  PubMed  PubMed Central  Google Scholar 

  29. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31(9):814–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6(3):610–618

    Article  CAS  PubMed  Google Scholar 

  31. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194–2200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2013) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42(D1):D199–D205

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28(1):27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40(3-4):237–264

    Article  Google Scholar 

  35. Koizumi Y, Kojima H, Oguri K, Kitazato H, Fukui M (2004) Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rDNA-based analysis, and related to physicochemical gradients. Environ Microbiol 6(6):622–637

    Article  CAS  PubMed  Google Scholar 

  36. Yoshimura KM (2019) Influences of particulate matter transport, export, and sedimentation on microbial community ecology. Yoshimura, Kristin Michelle. University of Delaware, ProQuest Dissertations Publishing, 2019. 13859788

  37. Abia ALK, James C, Ubomba-Jaswa E, Benteke Momba MN (2017) Microbial remobilisation on riverbed sediment disturbance in experimental flumes and a human-impacted river: implication for water resource management and public health in developing sub-Saharan African countries. Int J Environ Res Public Health 14(3):306

    Article  PubMed Central  Google Scholar 

  38. Giannuzzi L (2018) Cyanobacteria growth kinetics. Algae, Yee Keung Wong, IntechOpen. https://doi.org/10.5772/intechopen.81545

  39. Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PS, Reitenga KG, Xie G, Poulton NJ, Gomez ML, Masland DE (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 7(4):e35314

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF (2020) Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 5:1026–1039. https://doi.org/10.1038/s41564-020-0720-2

  41. Casadevall A, L-a P (2014) Microbiology: ditch the term pathogen. Nature News 516(7530):165–166

    Article  CAS  Google Scholar 

  42. Anudit C, Kooltheat N, Potup P, Sranujit RP, Usuwanthim K (2016) Nosocomial infection of multidrug-resistant Acinetobacter baumannii in Thailand. Am J Infect Control 44(10):1161–1163

    Article  PubMed  Google Scholar 

  43. Joly-Guillou ML (2005) Clinical impact and pathogenicity of Acinetobacter. Clin Microbiol Infect 11(11):868–873

    Article  PubMed  Google Scholar 

  44. Garnacho-Montero J, Amaya-Villar R (2010) Multiresistant Acinetobacter baumannii infections: epidemiology and management. Curr Opin Infect Dis 23(4):332–339

    Article  PubMed  Google Scholar 

  45. Ramadan N (2016) Prevalence of legionella among pneumonia patients and environmental water samples in an Egyptian University Hospital. Intern Arabic J Antimicrob Agents 6(2)

  46. El-Liethya MA, Hemdana BA, El-Shatouryb EH, Abou-Zeidb MA, Samhana FA, El-Taweela GE (2016) Prevalence of Legionella spp. and Helicobacter pylori in different water resources in Egypt. Egyptian Journal of Environmental Research 4

  47. Loeffelholz MJ (2014) Respiratory infections, an issue of clinics in laboratory medicine, vol 34-2, 1st edn. University of Texas Medical Branch Galveston, Texas. Imprint: Elsevier. Published Date: 3rd June 2014

  48. Albarral V, Sanglas A, Palau M, Miñana-Galbis D, Fusté MC (2016) Potential pathogenicity of Aeromonas hydrophila complex strains isolated from clinical, food, and environmental sources. Can J Microbiol 62(4):296–306

    Article  CAS  PubMed  Google Scholar 

  49. Austin B, Austin DA (2016) Bacterial fish pathogens: disease of farmed and wild fish, 6th ed. Springer International Publishing, p 732. https://doi.org/10.1007/978-3-319-32674-0

  50. Rogalla D, Bomar PA (2020) Listeria Monocytogenes. [Updated 2020 Jul 10]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing. Available from: https://www.ncbi.nlm.nih.gov/books/NBK534838/

  51. WHO (2018) Listeriosis: fact sheet. Geneva: World Health Organization, 2018. http://www.who.int/mediacentre/factsheets/listeriosis/en/ (accessed 20 February 2018)

  52. de Noordhout CM, Devleesschauwer B, Angulo FJ, Verbeke G, Haagsma J, Kirk M, Havelaar A, Speybroeck N (2014) The global burden of listeriosis: a systematic review and meta-analysis. Lancet Infect Dis 14(11):1073–1082

    Article  PubMed  PubMed Central  Google Scholar 

  53. Gad MA, Al-Herrawy AZ (2016) Real-time PCR detection of Acanthamoeba species in the Egyptian aquatic environment. Int J Pharma Clin Res 8:1510–1515

    Google Scholar 

  54. Rastogi RP, Madamwar D, Incharoensakdi A (2015) Bloom dynamics of cyanobacteria and their toxins: environmental health impacts and mitigation strategies. Front Microbiol 6:1254

    Article  PubMed  PubMed Central  Google Scholar 

  55. Kindaichi T, Yuri S, Ozaki N, Ohashi A (2012) Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor. Water Sci Technol 66(12):2556–2561

    Article  CAS  PubMed  Google Scholar 

  56. Florou-Paneri P, Christaki E, Bonos E (2013) Lactic acid bacteria as source of functional ingredients. In: Marcelino Kongo J (eds.) Lactic acid bacteria - R & D for food, health and livestock purposes. https://doi.org/10.5772/47766

Download references

Acknowledgments

The authors are deeply grateful to Prof. Ramy Karam Aziz, Chairperson of the Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, for providing critical insights and valuable feedback that greatly assisted the research.

Funding

This work has been partly supported by NSF-DEB grant 2016423 to NHY and MSE and by the Academy of Scientific Research and Technology (ASRT) JESOR Project #3046 to MSE and ASY.

Author information

Authors and Affiliations

  1. Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr-Eleini St, Cairo, 11562, Egypt

    Walaa A. Eraqi, Marwa T. ElRakaiby, Salwa A. Megahed & Aymen S. Yassin

  2. Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza, 12585, Egypt

    Salwa A. Megahed

  3. Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74074, USA

    Noha H. Yousef & Mostafa S. Elshahed

Authors
  1. Walaa A. Eraqi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marwa T. ElRakaiby
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Salwa A. Megahed
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Noha H. Yousef
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mostafa S. Elshahed
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Aymen S. Yassin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Aymen S. Yassin.

Ethics declarations

Conflict of Interest

All authors declare that they have no competing interests of any sort.

Supplementary Information

ESM 1

(DOCX 155 kb)

ESM 2

(TXT 2678 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Eraqi, W.A., ElRakaiby, M.T., Megahed, S.A. et al. Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis. Microb Ecol 82, 288–298 (2021). https://doi.org/10.1007/s00248-020-01674-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-020-01674-8

Keywords

Search

Navigation