Comparative Analysis of Microbial Community Structure and Composition across Tropical Freshwater Ecosystems Using 16S rRNA Metagenomics — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Comparative Analysis of Microbial Community Structure and Composition across Tropical Freshwater Ecosystems Using 16S rRNA Metagenomics
Godfrey Okoye University, Enugu, Nigeria
,
Godfrey Okoye University, Enugu, Nigeria
,
DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
,
DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
,
DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
,
DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
,
Godfrey Okoye University, Enugu, Nigeria
,
Department of Natural Sciences, Bowie State University, Bowie, MD, USA
1 Godfrey Okoye University, Enugu, Nigeria
2 Godfrey Okoye University, Enugu, Nigeria
3 DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
4 DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
5 DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
6 DNA Learning Center Nigeria, Ugwuomu-Nike, Enugu, Nigeria
7 Godfrey Okoye University, Enugu, Nigeria
8 Department of Natural Sciences, Bowie State University, Bowie, MD, USA
Understanding the microbial diversity of freshwater bodies provides insight into their trophic status, habitat type, and degree of contamination. This study represents the first attempt to evaluate the taxonomic composition and microbial diversity of three freshwater bodies (Iyiube Lake, Abala Lake, and Iyioku River) located in Enugu East, Nigeria. Genomic DNA was isolated from the collected water samples, and the compositions of the microbial communities were characterized using the 16S rRNA sequencing method. The results of metagenomics analysis identified a total of 31 phyla, 81 classes, 139 orders, 177 families, and 209 genera. The two dominant bacterial phyla identified in the present study are Proteobacteria and Acidobacteria. Additionally, other prevalent phyla identified are Chloroflexi, Bacteroidota, Verrucomicrobiota, Myxococcota, and Nitrospirota. Among the bacterial phyla present in the freshwater ecosystems studied, Fusobacteria was the least prevalent phylum, only detected in Abala Lake. Additional phyla unique to single freshwater bodies are Sumerlaeota, DTB120, Deferrisomatota, Hydrogenedentes, Elusimicrobiota, and NB1-j, suggesting niche differentiation. Thus, when compared to other freshwater bodies, Iyiube Lake exhibits the largest abundance of Acidobacteria, which may indicate anthropogenic influence because of high sewage deposit. This study provides the first baseline inventory of bacterial assemblages in these tropical freshwater systems, underscoring their ecological uniqueness and the potential of specific taxa as bioindicators for environmental monitoring and freshwater ecosystem restoration in the tropical regions.
Brar, B., Kumar, R., Sharma, D., Sharma, A.K., Thakur, K., Mahajan, D., et al. (2023) Metagenomic Analysis Reveals Diverse Microbial Community and Potential Functional Roles in Baner Rivulet, India. Journal of Genetic Engineering and Biotechnology , 21, Article 147. https://doi.org/10.1186/s43141-023-00601-x
Sigee, D.C. (2004) Freshwater Microbiology: Biodiversity and Dynamic Interactions of Microorganisms in the Freshwater Environment. John Wiley & Sons Ltd. https://doi.org/10.1002/0470011254
Alotaibi, M.O., Mohammed, A.E. and Eltom, K.H. (2022) Metagenomic Analysis of Bacterial Communities of Wadi Namar Lake, Riyadh, Saudi Arabia. Saudi Journal of Biological Sciences , 29, 3749-3758. https://doi.org/10.1016/j.sjbs.2022.03.001
Halvorson, H.M., Wyatt, K.H. and Kuehn, K.A. (2020) Ecological Significance of Autotroph Heterotroph Microbial Interactions in Freshwaters. Freshwater Biology , 65, 1183-1188.
Harrison, I.J., Green, P.A., Farrell, T.A., Juffe‐Bignoli, D., Sáenz, L. and Vörösmarty, C.J. (2016) Protected Areas and Freshwater Provisioning: A Global Assessment of Freshwater Provision, Threats and Management Strategies to Support Human Water Security. Aquatic Conservation : Marine and Freshwater Ecosystems , 26, 103-120. https://doi.org/10.1002/aqc.2652
Fierer, N., Leff, J.W., Adams, B.J., Nielsen, U.N., Bates, S.T., Lauber, C.L., et al. (2012) Cross-biome Metagenomic Analyses of Soil Microbial Communities and Their Functional Attributes. Proceedings of the National Academy of Sciences , 109, 21390-21395. https://doi.org/10.1073/pnas.1215210110
Lynch, M.D.J. and Neufeld, J.D. (2015) Ecology and Exploration of the Rare Biosphere. Nature Reviews Microbiology , 13, 217-229. https://doi.org/10.1038/nrmicro3400
Shade, A., Peter, H., Allison, S.D., Baho, D.L., Berga, M., Bürgmann, H., et al. (2012) Fundamentals of Microbial Community Resistance and Resilience. Frontiers in Microbiology , 3, Article No. 417. https://doi.org/10.3389/fmicb.2012.00417
Vartoukian, S.R., Palmer, R.M. and Wade, W.G. (2010) Strategies for Culture of ‘Unculturable’ Bacteria. FEMS Microbiology Letters , 309, 1-7. https://doi.org/10.1111/j.1574-6968.2010.02000.x
Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J. and Goodman, R.M. (1998) Molecular Biological Access to the Chemistry of Unknown Soil Microbes: A New Frontier for Natural Products. Chemistry & Biology , 5, R245-R249. https://doi.org/10.1016/s1074-5521(98)90108-9
Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., et al. (2004) Community Structure and Metabolism through Reconstruction of Microbial Genomes from the Environment. Nature , 428, 37-43. https://doi.org/10.1038/nature02340
Vareda, J.P., Valente, A.J.M. and Durães, L. (2019) Assessment of Heavy Metal Pollution from Anthropogenic Activities and Remediation Strategies: A Review. Journal of Environmental Management , 246, 101-118. https://doi.org/10.1016/j.jenvman.2019.05.126
Chanamé-Zapata, F., Custodio, M., Poma-Chávez, C. and Cruz, A.H.L. (2020) Nutrient Concentrations and Trophic State of Three Andean Lakes from Junín, Perú. Ambiente e Agua — An Interdisciplinary Journal of Applied Science , 15, 1-9. https://doi.org/10.4136/ambi-agua.2525
Hänfling, B., Lawson Handley, L., Read, D.S., Hahn, C., Li, J., Nichols, P., et al. (2016) Environmentaldnametabarcoding of Lake Fish Communities Reflects Long‐Term Data from Established Survey Methods. Molecular Ecology , 25, 3101-3119. https://doi.org/10.1111/mec.13660
Gómez, G.D. and Balcázar, J.L. (2008) A Review on the Interactions between Gut Microbiota and Innate Immunity of Fish: Table 1. FEMS Immunology & Medical Microbiology , 52, 145-154. https://doi.org/10.1111/j.1574-695x.2007.00343.x
Wilkins, L.G.E., Ettinger, C.L., Jospin, G. and Eisen, J.A. (2019) Metagenome-Assembled Genomes Provide New Insight into the Microbial Diversity of Two Thermal Pools in Kamchatka, Russia. Scientific Reports , 9, Article No. 3053. https://doi.org/10.1038/s41598-019-39576-6
Llorens-Marès, T., Yooseph, S., Goll, J., Hoffman, J., Vila-Costa, M., Borrego, C.M., et al. (2015) Connecting Biodiversity and Potential Functional Role in Modern Euxinic Environments by Microbial Metagenomics. The ISME Journal , 9, 1648-1661. https://doi.org/10.1038/ismej.2014.254
Ghai, R., Rodŕíguez-Valera, F., McMahon, K.D., Toyama, D., Rinke, R., Cristina Souza de Oliveira, T., et al. (2011) Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River. PLOS ONE , 6, e23785. https://doi.org/10.1371/journal.pone.0023785
Pester, M., Rattei, T., Flechl, S., Gröngröft, A., Richter, A., Overmann, J., et al. (2012) amoa ‐based Consensus Phylogeny of Ammonia‐oxidizing Archaea and Deep Sequencing of Amoa Genes from Soils of Four Different Geographic Regions. Environmental Microbiology , 14, 525-539. https://doi.org/10.1111/j.1462-2920.2011.02666.x
Quince, C., Walker, A.W., Simpson, J.T., Loman, N.J. and Segata, N. (2017) Shotgun Metagenomics, from Sampling to Analysis. Nature Biotechnology , 35, 833-844. https://doi.org/10.1038/nbt.3935
Alkali, M., Okwete, N.J. and Kasimu, S.U. (2021) Effect of Chemical Fertilizer Usage on the Quality of Agricultural Soils in Ugwuomu Nike, Enugu East Local Government Area of Enugu State, Nigeria. International Journal of Agricultural Technology , 22, No. 1.
Bolyen, E., et al. (2019) Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2. Nature Biotechnology , 37, 852-857.
Han, B., Addo, F.G., Mu, X., Zhang, L., Zhang, S., Lv, X., et al. (2019) Epiphytic Bacterial Community Shift Drives the Nutrient Cycle during Potamogeton Malaianus Decomposition. Chemosphere , 236, Article 124253. https://doi.org/10.1016/j.chemosphere.2019.06.223
Moser, K.A., Baron, J.S., Brahney, J., Oleksy, I.A., Saros, J.E., Hundey, E.J., et al. (2019) Mountain Lakes: Eyes on Global Environmental Change. Global and Planetary Change , 178, 77-95. https://doi.org/10.1016/j.gloplacha.2019.04.001
Lin, S., Shen, S., Zhou, A. and Lyu, H. (2021) Assessment and Management of Lake Eutrophication: A Case Study in Lake Erhai, China. Science of The Total Environment , 751, Article 141618. https://doi.org/10.1016/j.scitotenv.2020.141618
Wang, Y., Sheng, H., He, Y., Wu, J., Jiang, Y., Tam, N.F., et al. (2012) Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags. Applied and Environmental Microbiology , 78, 8264-8271. https://doi.org/10.1128/aem.01821-12
Qin, Y., Hou, J., Deng, M., Liu, Q., Wu, C., Ji, Y., et al. (2016) Bacterial Abundance and Diversity in Pond Water Supplied with Different Feeds. Scientific Reports , 6, Article No. 35232. https://doi.org/10.1038/srep35232
Md Lasim, A., Mohd Ngesom, A.M., Nathan, S., Abdul Razak, F., Abdul Halim, M., Mohd-Saleh, W., et al. (2024) Bacterial Community Profiles within the Water Samples of Leptospirosis Outbreak Areas. Peer J , 12, e17096. https://doi.org/10.7717/peerj.17096
Adedire, D.E., Jimoh, A.O., Kashim-Bello, Z., Shuaibu, B.A.W., Popoola, O.A., Pate, K.I., et al. (2022) Microbiome Diversity Analysis of the Bacterial Community in Idah River, Kogi State, Nigeria. Advances in Microbiology , 12, 343-362. https://doi.org/10.4236/aim.2022.125025
Krishna, M., Gupta, S., Delgado-Baquerizo, M., Morriën, E., Garkoti, S.C., Chaturvedi, R., et al. (2020) Successional Trajectory of Bacterial Communities in Soil Are Shaped by Plant-Driven Changes during Secondary Succession. Scientific Reports , 10, Article No. 9864. https://doi.org/10.1038/s41598-020-66638-x
Betiku, O.C., Sarjeant, K.C., Ngatia, L.W., Aghimien, M.O., Odewumi, C.O. and Latinwo, L.M. (2021) Evaluation of Microbial Diversity of Three Recreational Water Bodies Using 16S rRNA Metagenomic Approach. Science of The Total Environment , 771, Article 144773. https://doi.org/10.1016/j.scitotenv.2020.144773
Marín, I. and Arahal, D.R. (2014) Class Gammaproteobacteria. In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E. and Thompson, F., Eds., The Prokaryotes : Gammaproteobacteria , Springer, 1-3.
Núñez Salazar, R., Vizuete, K., Chóez-Guaranda, I., Molina, F., Herrera, C. and Vera, P. (2020) Bacterial Community Structure and Environmental Conditions in Shrimp-culture Ponds with Varying Salinity and pH. Aquaculture Reports , 16, Article 100275.
Wong, H.L., Bulzu, P., Ghai, R., Chiriac, M. and Salcher, M.M. (2024) Ubiquitous Genome Streamlined Acidobacteriota in Freshwater Environments. ISME Communications , 4, ycae124. https://doi.org/10.1093/ismeco/ycae124
Gonçalves, O.S., Fernandes, A.S., Tupy, S.M., Ferreira, T.G., Almeida, L.N., Creevey, C.J., et al. (2024) Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum. Soil Biology and Biochemistry , 192, Article 109369. https://doi.org/10.1016/j.soilbio.2024.109369
Flieder, M., Buongiorno, J., Herbold, C.W., Hausmann, B., Rattei, T., Lloyd, K.G., et al. (2021) Novel Taxa of Acidobacteriota Implicated in Seafloor Sulfur Cycling. The ISME Journal , 15, 3159-3180. https://doi.org/10.1038/s41396-021-00992-0
Nunoura, T., Hirayama, H., Takami, H., Oida, H., Nishi, S., Shimamura, S., et al. (2005) Genetic and Functional Properties of Uncultivated Thermophilic Crenarchaeotes from a Subsurface Gold Mine as Revealed by Analysis of Genome Fragments. Environmental Microbiology , 7, 1967-1984. https://doi.org/10.1111/j.1462-2920.2005.00881.x
Ghezzi, D., Mangiaterra, G., Scardino, A., Fehervari, M., Magnani, M., Citterio, B., et al. (2024) Characterization of Bacterial Communities Associated with Seabed Sediments in Offshore and Nearshore Sites to Improve Microbiologically Influenced Corrosion Mitigation on Marine Infrastructures. PLOS ONE , 19, e0309971. https://doi.org/10.1371/journal.pone.0309971
Tessler, M., Brugler, M.R., DeSalle, R., Hersch, R., Velho, L.F.M., Segovia, B.T., et al. (2017) A Global Edna Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil. Microbial Ecology , 73, 61-74. https://doi.org/10.1007/s00248-016-0834-5
Iliev, I., Yahubyan, G., Marhova, M., et al. (2017) Metagenomic Profiling of the Microbial Freshwater Communities in Two Bulgarian Reservoirs. Journal of Basic Microbiology , 57, 669-679.
Cardman, Z., Arnosti, C., Durbin, A., Ziervogel, K., Cox, C., Steen, A.D., et al. (2014) Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard. Applied and Environmental Microbiology , 80, 3749-3756. https://doi.org/10.1128/aem.00899-14
Yadav, N. and Sharma, S. (2020) Pollution Shapes the Bacterial Community of a River: A Case Study. International Journal of Environmental Science and Technology , 17, 2003-2016. https://doi.org/10.1007/s13762-019-02474-5
Fang, L., Chen, L., Liu, Y., Tao, W., Zhang, Z., Liu, H., et al. (2015) Planktonic and Sedimentary Bacterial Diversity of Lake Sayram in Summer. MicrobiologyOpen , 4, 814-825. https://doi.org/10.1002/mbo3.281
McAllister, S.M., Moore, R.M., Gartman, A., Chan, C.S. and Luther, G.W. (2021) Novel Uncultured DTB120 Bacteria from Iron-Oxidizing Microbial Mats at Lōʻihi Seamount Revealed by Genome-Resolved Metagenomics and Meta Transcriptomics. ISME Journal , 15, 1184-1199.
Kim, P.S., Shin, N., Lee, J., Kim, M., Whon, T.W., Hyun, D., et al. (2021) Host Habitat Is the Major Determinant of the Gut Microbiome of Fish. Microbiome , 9, Article No. 166. https://doi.org/10.1186/s40168-021-01113-x