Microbial Diversity, and Structure of Coastal Water Bodies from Some Cholera-prone Communities in Rivers State, Nigeria

Chidimma Anthonia Azike^1, , Vivian Nkemkanma Agi¹, Ollor Amba Ollor¹, Easter Godwin Nwokah¹, Chinyere Ihuarulam Okoro² and Confidence Kinikanwo Wachukwu¹

¹Department of Medical Laboratory Science, Rivers State University

²Department of Microbiology/ Parasitology, Federal Teaching Hospital Owerri, Imo State

Cite this paper:
Chidimma Anthonia Azike, Vivian Nkemkanma Agi, Ollor Amba Ollor, Easter Godwin Nwokah, Chinyere Ihuarulam Okoro and Confidence Kinikanwo Wachukwu. Microbial Diversity, and Structure of Coastal Water Bodies from Some Cholera-prone Communities in Rivers State, Nigeria. American Journal of Epidemiology and Infectious Disease. 2024; 12(1):1-13. doi: 10.12691/ajeid-12-1-1

Abstract

Background: This study aimed to determine the microbial diversity and Community Structure of Coastal water bodies from some cholera-prone communities in Rivers State. Methods: Water samples were collected from water bodies located in six different cholera prone coastal communities in Rivers state three times each with the determination of coordinates each time using Global Positioning System (GPS). At each collection point, in-situ physicochemical parameters of water sources were determined using H198194, H198195, and H198196 multiparameter meters (Hanna Instrument Inc, USA). The water samples were collected using a sterilized container of 750ml capacity (75cl). DNA was extracted from each water sample collected. The extracted DNA from the water samples were sequenced by Illumina HighSeq by InqabaBiotec, South Africa. The sequencing library was prepared by random fragmentation of the DNA, followed by 5′and 3′ adapter ligation. Adapter-ligated fragments were then PCR-amplified and gel purified. For cluster generation, the library was loaded into a flow cell where fragments were captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment was then amplified in to distinct, clonal clusters through bridge amplification. When cluster generation was complete, the templates were sequenced using Illumina MiSeq SBS technology. Results: The microbial communities in the coastal water studied are highly diversified. The microorganisms are generally classified into kingdoms containing bacteria, protozoa, viruses, archaea, fungi, and Plantae. For all the coastal waters, kingdom bacteria is common with varying percentage reads which ranged from 45835 reads (46.64%) in Bonny river to 263985 reads (99.71%) in Kaa river. Protozoa were identified in addition to other microbial communities in Andoni and Kaa rivers, both in the South-east senatorial district of Rivers State. The number of viruses detected is more in the Chukwu-Ama river in Ogu/bolo with total reads of 384 (0.25% of microbes present). In addition to other kingdoms present in the Okirika River, fungi were also detected. Alpha diversity of bacterial species across the three regions investigated showed no significant difference while that of individual samples was significantly different at P≤ 0.05 using observed features, Shannon diversity index, Faith’s phylogenetic diversity and Pielou’s evenness tools. Bray-Curtis dissimilarity between the bacterial communities’ structures in the three zones investigated did not reveal distinct differentiation in multivariate space. The observed clustering pattern of samples within the PCoA (Principal coordinate analysis) plot was found to be non-significantly (FDR-adjusted p>0.05) different among the zones in Rivers State (PERMANOVA R2 = 43.3%, p = 0.07). The ASVs detected in all zones of Rivers state spanned 15 phyla (Rivers East = 13; Rivers South-east = 13; Rivers West = 10). Actinobacteriota was the most relatively abundant phyla in both Rivers East (43.9%) and Rivers South-east (35.5%) while Firmicutes (36.2%) was the most abundant phyla in Rivers West. Conclusion: This study has shown that microbial communities present in coastal waters are highly diversified with unknown and unassigned microorganisms detected from all the coastal water examined, showing that these waters are hubs for highly potential microorganisms that could be inimical to human health.

Keywords:
microbial diversity Microbial Structure coastal water cholera community

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References:

[1]	Panizzon, J. P., Pilz, J., Harry, L.,Knaak, N. R., Renata, C., Ziegler, E. R. &Fiuza, L. M. (2015). Microbial dioversity: Relevance and relationship between environmental conservation and human health. Brazilian Archives of Biology and Technology, 58(1), 137-145.
[2]	Qin, J., Li, R., Raes, J., Arumugam, M.,Burgdorf, K. S., Manichanh, C., Nielson, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., Tap, J., Lepage, P., Bertalan, M., Batto, J., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H. B., Pelletier, E., Renault, P.,Sicheritz-ponten, T., Turner, K., Zhu, H., Yu, C., Jian, M., Zhou, Y., Li, Y., Zhang, X., Qin, N., Yang, H., Wang, J., Brunak, S., Dore, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork. P., Ehrlich, D. & Mende, D. R. (2010). A human gut microbiota gene catalog established by metagenomics sequencing. Nature, 464, 59-65.
[3]	Kane, M., Case, L. K., Kopasikie, K., Kozlova, A., MacDearmid, C., Chervonsky, A.V. &Golovkina, T.V. (2011). Successful transmission of a retrovirus depends on the commercial microbiota. Science, 334(6053), 245-249.
[4]	Kembel, S. W., Eisen, J. A., Pollard, K. S. & Green, J. L. (2011). The phylogenetic diversity of metagenomes. Public Library of Science One, 6(8), 1-9.
[5]	Janda, J. M. & Abbott, S. L. (2007). 16SrRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Journal of Clinical Microbiology, 45(9), 2761- 2764.
[6]	Valcheva, V., Mokrousov, I., Narvsakaya, O., Rastogi, N. & Markova, N. (2008). Molecular snapshot of drug resitant and drug susceptible Mycobacterium tuberculosis strains circulating in Bulgaria. Infection, Genetic and Evolution, 8(5), 657-663.
[7]	Greenberg, A. (1985). Standard method for the examination of water and wastewater, (18th Ed.).Washington, DC: USA. American Public Health Association.
[8]	Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodriguez, A.M., Chase, J., Cope, E.K., Da Silva, R., Diener, C., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibbons, S.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G.A., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B.D., Kang, K.B., Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G., Lee, J., Ley, R., Liu, Y.X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, A.T., Nava-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, M.S.,
[9]	Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A. & Holmes, S.P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. National Methods, 13, 581-583.
[10]	Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H., Szoecs, E. & Wagner, H. (2019). Community Ecology Package.
[11]	Qin, Y., Hou, J., Deng, M., Liu, Q., Wu, C., Ji, Y., & He, X. (2016). Bacterial abundance and diversity in pond water supplied with different feeds. Scientific Reports, 6, 35232.
[12]	Ollor, A.O., Agi, V.N., Aleru, C.P., Abbey, S.D., Ebere, N. &Elenwo, E. C. (2018). The bacteriological and physicochemical qualities of of Koru-Ama Bonny (marine) and Penee (fresh) in coastal area of Rivers State. European Journal of Pharmaceutical and MedicalResearch, 5(3), 50-56.
[13]	Sowani, H., Kulkarni, M., Zinjarde, S. &Javdekar, V. (2017). Gordonia and related genera as opportunistic human pathogens causing infections of skin, soft tissues and bone. Editors: KaterynaKon, Mahendra Rai, In Clinical Microbiology: Diagnosis, treatment and prophylaxis of infections. The Microbiology of skin, soft tissues, bone and joint infections, Academic Press, volume 2, 105-121.
[14]	Barka, E.A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Klenk, H., Clement, C., Ouhdouch, Y. & van Wezel, G.P. (2016). Taxonomy, physiology and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews, 80(1), 1-43.
[15]	Rizzatti, G., Lopetusa, L.R., Gibiino, G., Binda, C. &Gasbarrini, A. (2017). Proteobacteria: A common factor in human diseases. Biomedical Research International, 1-7.
[16]	Ouattara, M. ,Zongo, F. &Zongo, B. (2021) Species Diversity of Cyanobacteria and Desmids of a Drinking Water Source under Anthropogenic Pressure, and Their Implication in Toxin Production and Water Quality in Sub-Saharan Africa (Burkina Faso, Western Africa). Journal of Water Resource and Protection, 13, 1000-1023.
[17]	Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., Rattei, T., Damsté, J. S., Spieck, E., Le Paslier, D. &Daims, H. (2010). A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proceedings of the National Academy of Sciences of the United States of America, 107(30), 13479–13484.
[18]	Ushiki, N., Fujitani, H., Shimada, Y., Morohoshi, T., Sekiguchi, Y. &Tsuneda, S. (2018). Genomics analysis of two phylogenetically distinct Nitrospira species reveals their genomic plasticity and functional diversity. Frontiers in Microbiology, 8, 26-37.
[19]	Muwawa, E.M., Obieze, C.C., Makonde, H.M., Jefwa, J.M., Kahindi, J.H.P. &Khasa, D.P. (2021).16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya. PLoS ONE,16(3),12-18.
[20]	Hou, D., Huang, Z., Zeng, S., Liu, J., Wei, D., Deng, X., Weng, S., He, Z. & He, J. (2017). Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems. Frontiers in Microbiology, 1-18.
[21]	Louca, S., Parfrey, L. W. &Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science, 353, 1272–1277.