Importance of Mapping the Bacterial Community Dynamics in Inland Waters
Emine Gözde Özbayram, Zuhal Zengin, Latife KökerThe bacterial community has a crucial role in the ecosystem’s well-being, contributing to biogeochemical cycles, including carbon, nitrogen, and phosphorus as well as organic matter degradations. The community pattern differs spatially due to various factors such as distinctive environmental conditions, land usage, anthropogenic activities, etc. The use of molecular biology tools is becoming a key approach to evaluating complex bacterial community structures. The advanced metagenomics databases, powerful bioinformatics, and statistical tools enable us to get valuable insights into bacterial metabolic functions. Understanding the complexity of bacterial communities is vitally important to assess the impacts of certain niches on the ecosystem. This chapter focuses on the bacterial communities in freshwater resources and reveal their diversity in these ecosystems.
References
- Acharya, K., Blackburn, A., Mohammed, J., Haile, A. T., Hiruy, A. M., & Werner, D. (2020). Metagenomic water quality monitoring with a portable laboratory. Water Research, 184, 116112. google scholar
- Acharya, K., Khanal, S., Pantha, K., Amatya, N., Davenport, R. J., & Werner, D. (2019). A comparative assess-ment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality. Scientific Reports, 9(1), 15726. google scholar
- Akçaalan, R., Albay, M., Koker, L., Baudart, J., Guillebault, D., Fischer, S., Weigel, W., & Medlin, L. K. (2018). Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey. Environmental Monitoring and Assessment, 190, 1-21. google scholar
- Akçaalan, R., Köker, L., Gürevin, C., & Albay, M. (2014) Planktothrix rubescens: a perennial presence and toxicity in Lake Sapanca. Turkish Journal of Botany, 38(4), Article 15. google scholar
- Albay, M., Matthiensen, A., & Codd, G. A. (2005). Occurrence of toxic blue-green algae in the Kucukcekmece lagoon (Istanbul, Turkey). Environmental Toxicology: An International Journal, 20(3), 277-284. google scholar
- Alotaibi, M. O., Mohammed, A. E., & Eltom, K. H. (2022). Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia. Saudi Journal of Biological Sciences, 29(5), 3749-3758. google scholar
- Azli, B., Razak, M. N., Omar, A. R., Mohd Zain, N. A., Abdul Razak, F., & Nurulfiza, I. (2022). Metagenomics insights into the microbial diversity and microbiome network analysis on the heterogeneity of influent to effluent water. Frontiers in Microbiology, 13, 779196. google scholar
- Bandh, S. A., Shafi, S., Shameem, N., Dar, R., Kamili, A. N., & Ganai, B. A. (2019). Spatio-temporal patterns of bacterial diversity along environmental gradients and bacterial attachment to organic aggregates. In Freshwater Microbiology (pp. 137-174). Academic Press. google scholar
- Barooah, M., Goswami, G., Hazarika, D. J., & Kangabam, R. (2021). High-Throughput Analysis to Decipher Bacterial Diversity and their Functional Properties in Freshwater Bodies. Microbial Metatranscriptomics Belowground, 511-542. google scholar
- Behera, B. K., Sahu, P., Rout, A. K., Parida, P. K., Sarkar, D. J., Kaushik, N. K., ... & Mohapatra, T. (2021). Exploring microbiome from sediments of River Ganga using a metagenomic approach. Aquatic Ecosystem Health & Management, 24(4), 12-22. google scholar
- Biddanda, B., Ogdahl, M., & Cotner, J. (2001). Dominance of bacterial metabolism in oligotrophic relative to eutrophic waters. Limnology and Oceanography, 46(3), 730-739. google scholar
- Cai, T., Jiang, L., Yang, C., & Huang, K. (2006). Application of real-time PCR for quantitative detection of Vibrio parahaemolyticus from seafood in eastern China. FEMS Immunology & Medical Microbiology, 46(2), 180-186. google scholar
- Carlson, R. E. (1977). A trophic state index for lakes 1. Limnology and Oceanography, 22(2), 361-369. google scholar
- Chakraborty, J., Rajput, V., Sapkale, V., Kamble, S., & Dharne, M. (2021). Spatio-temporal resolution of taxono-mic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation. Chemosphere, 264, 128574. google scholar
- Chen, Y., Li, S., Xu, X., Ma, M., Mi, T., Zhen, Y., & Yu, Z. (2021). Characterization of microbial communities in sediments of the South Yellow Sea. Journal of Oceanology and Limnology, 39(3), 846-864. google scholar
- Cowan, D., Meyer, Q., Stafford, W., Muyanga, S., Cameron, R., & Wittwer, P. (2005). Metagenomic gene dis-covery: past, present and future. TRENDS in Biotechnology, 23(6), 321-329. google scholar
- Çınar, S., Çakır, E., & Mutlu, M. B. (2022). Characterization of Cultivable Diversity and Carbon Substrate Utilization in the Sediments of Lake Tuz. Eurasian Soil Science, 55(9), 1248-1257. google scholar
- Çiftçi Türetken, P. S., Altuğ, G., Çardak, M., & Güneş, K. (2019). Bacteriological quality, heavy metal and anti-biotic resistance in Sapanca Lake, Turkey. Environmental Monitoring and Assessment, 191, 1-12. google scholar
- Fisher, M. M., Klug, J. L., Lauster, G., Newton, M., & Triplett, E. W. (2000). Effects of resources and trophic interactions on freshwater bacterioplankton diversity. Microbial Ecology, 40, 125-138. google scholar
- Davis, B. C., Brown, C., Gupta, S., Calarco, J., Liguori, K., Milligan, E., ... & Keenum, I. (2023). Recommenda-tions for the use of metagenomics for routine monitoring of antibiotic resistance in wastewater and impacted aquatic environments. Critical Reviews in Environmental Science and Technology, 1-26. google scholar
- Ersoy Omeroglu, E., Sudagidan, M., Yurt, M. N. Z., Tasbasi, B. B., Acar, E. E., & Ozalp, V. C. (2021). Micro-bial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples. Scientific Reports, 11(1), 18364. google scholar
- Garcia, S. L., Salka, I., Grossart, H. P., & Warnecke, F. (2013). Depth-discrete profiles of bacterial communities reveal pronounced spatio-temporal dynamics related to lake stratification. Environmental Microbiology Reports, 5(4), 549-555. google scholar
- Garner, E., Davis, B. C., Milligan, E., Blair, M. F., Keenum, I., Maile-Moskowitz, A., Pan, J., Gnegy, M., Li-guori, K., Gupta, S., Prussin, A., Marr, L., Heath, L., Vikesland, P., Zhang, L., & Pruden, A. (2021). Next generation sequencing approaches to evaluate water and wastewater quality. Water Research, 194, 116907. google scholar
- Ghilamicael, A. M., Boga, H. I., Anami, S. E., Mehari, T., & Budambula, N. L. (2018). Potential human pathogenic bacteria in five hot springs in Eritrea revealed by next generation sequencing. PLoS One, 13(3), e0194554. google scholar
- Grossart, H. P., Massana, R., McMahon, K. D., & Walsh, D. A. (2020). Linking metagenomics to aquatic mic-robial ecology and biogeochemical cycles. Limnology and Oceanography, 65, S2-S20. google scholar
- Güven, K., Mutlu, M. B., Çırpan, C., & Kutlu, H. M. (2013). Isolation and identification of selenite reducing archaea from Tuz (salt) Lake in Turkey. Journal of Basic Microbiology, 53(5), 397-401. google scholar
- Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry & Biology, 5(10), R245-R249. google scholar
- Haro-Moreno, J. M., Cabello-Yeves, P. J., Garcillan-Barcia, M. P., Zakharenko, A., Zemskaya, T. I., & Rodri-guez-Valera, F. (2023). A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics. Environmental Microbiome, 18(1), 1-12. google scholar
- Hendrayanti, D., Prihantini, N. B., Ningsih, F., & Maulana, F. (2023). Next Generation Sequencing (NGS) for Cyanobacterial study in Agung and Sunter Barat Lakes, North Jakarta, Indonesia. Biodiversitas Journal of Biological Diversity, 24(2). google scholar
- Hoke, A., Woodhouse, J., Zoccarato, L., McCarthy, V., de Eyto, E., Caldero-Pascual, M., Geffroy, E., Dillane, M., Grossart, H.P., & Jennings, E. (2020). Impacts of extreme weather events on bacterial community com-position of a temperate humic Lake. Water, 12(10), 2757. google scholar
- Horner-Devine, M. C., Carney, K. M., & Bohannan, B. J. (2004). An ecological perspective on bacterial biodi-versity. Proceedings of the Royal Society of London. Series B: Biological Sciences, 271(1535), 113-122. google scholar
- Ji, B., Liang, J., Ma, Y., Zhu, L., & Liu, Y. (2019). Bacterial community and eutrophic index analysis of the East Lake. Environmental Pollution, 252, 682-688. google scholar
- Ji, B., Qin, H., Guo, S., Chen, W., Zhang, X., & Liang, J. (2018). Bacterial communities of four adjacent fresh lakes at different trophic status. Ecotoxicology and Environmental Safety, 157, 388-394. google scholar
- Jo, J. H., Kennedy, E. A., & Kong, H. H. (2016). Research techniques made simple: bacterial 16S ribosomal RNA gene sequencing in cutaneous research. Journal of Investigative Dermatology, 136(3), e23-e27. google scholar
- Karafistan, A., & Arik-Colakoglu, F. (2005). Physical, chemical and microbiological water quality of the Manyas Lake, Turkey. Mitigation and Adaptation Strategies for Global Change, 10, 127-143. google scholar
- Kheiri, R., Mehrshad, M., Pourbabaee, A. A., Ventosa, A., & Amoozegar, M. A. (2023). Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation. Scientific Reports, 13(1), 374. google scholar
- Köker, L., Akçaalan, R., Albay, M., & Neilan, B. A. (2017). Molecular detection of hepatotoxic cyanobacteria in inland water bodies of the Marmara Region, Turkey. Advances in Oceanography and Limnology, 8(1). google scholar
- Kumar, V., Kumar, S., & Singh, D. (2022). Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies. Extremophiles, 26(1), 3. google scholar
- Liu, X. J., Wen, W. J., Yang, X. X., Hu, H. Y., Ji, T. C., Liu, H. M., & Zhu, G. P. (2022). Metagenomics Analysis on Bacterial Communities Seasonal Diversity in the Urban Lake Jinghu, Central of China. Inland Water Biology, 15(4), 403-409. google scholar
- Llorens-Mares, T., Catalan, J., & Casamayor, E. O. (2020). Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial meta-genomics. Science of the Total Environment, 707, 135929. google scholar
- Motlagh, A. M., & Yang, Z. (2019). Detection and occurrence of indicator organisms and pathogens. Water Environment Research, 91(10), 1402-1408. google scholar
- Najar, I. N., Sherpa, M. T., Das, S., & Nagendra, T. (2019) Diversity analysis and metagenomic insights into theantibiotic resistance and metal resistances among Himalayan hot spring Bacteriobiome insinuating in-herent environmental baseline levels of antibiotic and metal tolerance. Journal of Global Antimicrobial Resistance, 21, 342-352. google scholar
- Nath, M., Bhatt, D., Bhargava, P., & Choudhary, D. K. (Eds.). (2021). Microbial Metatranscriptomics Be-lowground. Springer Singapore. ISBN: 978-981-15-9757-2. google scholar
- Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D., & Bertilsson, S. (2011). A guide to the natural history of freshwater lake bacteria. Microbiology and Molecular Biology Reviews, 75(1), 14-49. google scholar
- Nosalova, L., Kiskova, J., Fecskeova, L. K., Piknova, M., & Pristas, P. (2023). Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe). Current Microbiology, 80(5), 145. google scholar
- Ozbayram, E. G., Köker, L., Çam, A. O., Akçaalan, R., & Albay, M. (2022a). Temporal and Spatial Variations of the Bacterial Diversity in a Deep Alkaline Lake. Water, 14(24), 4097. google scholar
- Ozbayram, E. G., Akcaalan, R., Isinibilir, M., & Albay, M. (2022b). Insights into the bacterial community structure of marine mucilage by metabarcoding. Environmental Science and Pollution Research, 29(35), 53249-53258. google scholar
- Ozbayram, E. G., Koker, L., Akçaalan, R., Aydın, F., Ertürk, A., Ince, O., & Albay, M. (2021). Contrasting the water quality and bacterial community patterns in shallow and deep lakes: Manyas vs. Iznik. Environmental Management, 67(3), 506-512. google scholar
- Özbayram, E. G., Miraloğlu, İ. H., & Bahar, İ. (2021). Assessment of microbial community diversity in lakes of İğneada floodplain forest by metabarcoding approach. Aquatic Research, 4(4), 304-312. google scholar
- Özbayram, E. G., Köker, L., Akcaalan, R., Orhan, İ., & Albay, M. (2020). Bacterial Community Composition of Sapanca Lake During a Cyanobacterial Bloom. Aquatic Sciences and Engineering, 35(2), 52-56. google scholar
- Pace, N. R., Stahl, D. A., Lane, D. J., & Olsen, G. J. (1986). The analysis of natural microbial populations by ribosomal RNA sequences. Advances in Microbial Ecology, 1-55. google scholar
- Pellegrinetti, T. A., Cotta, S. R., Sarmento, H., Costa, J. S., Delbaje, E., Montes, C. R., ... & Fiore, M. F. (2022). Bacterial communities along environmental gradients in tropical soda lakes. Microbial Ecology, 1-12. google scholar
- Perez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020). Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microbial Genomics, 6(8). google scholar
- Poyraz, N., & Mutlu, M. B. (2017). Determination of Prokaryotic Diversity of Salda Lake By Next Generation Sequencing Method. Journal of the Institute of Science and Technology, 7(3), 99-106. google scholar
- Prayogo, F. A., Budiharjo, A., Kusumaningrum, H. P., Wijanarka, W., Suprihadi, A., & Nurhayati, N. (2020). Metagenomic applications in exploration and development of novel enzymes from nature: a review. Journal of Genetic Engineering and Biotechnology, 18(1), 1-10. google scholar
- Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., ... & Loman, N. J. (2017). Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature Protocols, 12(6), 1261-1276. google scholar
- Ren, Z., Ma, K., Jia, X., Wang, Q., Zhang, C., & Li, X. (2022). Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area. Microbial Ecology, 1-12. google scholar
- Rösel, S., & Grossart, H. P. (2012). Contrasting dynamics in activity and community composition of free-living and particle-associated bacteria in spring. Aquatic Microbial Ecology, 66(2), 169-181. google scholar
- Salcher, M. M. (2014). Same same but different: ecological niche partitioning of planktonic freshwater prokar-yotes. Journal of Limnology, 73(1s), 74-87. google scholar
- Shahraki, A. H., Chaganti, S. R., & Heath, D. (2021). Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair’s large freshwater ecosystems. BMC Mic-robiology, 21, 1-15. google scholar
- Shang, Y., Wu, X., Wang, X., Wei, Q., Ma, S., Sun, G., Zhang,H., Wang, L., Dou, H., & Zhang, H. (2022). Factors affecting seasonal variation of microbial community structure in Hulun Lake, China. Science of the Total Environment, 805, 150294. google scholar
- Shen, M., Li, Q., Ren, M., Lin, Y., Wang, J., Chen, L., Li, T., & Zhao, J. (2019) Trophic status is associated with community structure and metabolic potential of planktonic microbiota in plateau lakes. Frontiers in Microbiology, 10, 1-15. google scholar
- Sanseverino, I., Pretto, P., Antonio, D. C., Lahm, A., Facca, C., Loos, R., Skejo, H., Beghi, A., Pandolfi, F., Genoni, P., & Lettieri, T. (2022). Metagenomics analysis to investigate the microbial communities and their functional profile during cyanobacterial blooms in Lake Varese. Microbial Ecology, 1-19. google scholar
- Shilei, Z., Yue, S., Tinglin, H., Ya, C., Xiao, Y., Zizhen, Z., Yang, L., Zaixing, L., Jiansheng, C., & Xiao, L. (2020). Reservoir water stratification and mixing affects microbial community structure and functional com-munity composition in a stratified drinking reservoir. Journal of Environmental Management, 267, 110456. google scholar
- Singh, A. K., Kumari, M., Sharma, N., Rai, A. K., & Singh, S. P. (2022). Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential. Current Genetics, 68(5-6), 565-579. google scholar
- Song, D., Huo, T., Zhang, Z., Cheng, L., Wang, L., Ming, K., ... & Du, X. (2022). Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors. International Journal of Environmental Research and Public Health, 19(24), 16870. google scholar
- Stocker, T. F., Qin, D., Plattner, G. K., Tignor, M. M. B., Allen, S. K., Boschung, J., Nauels, A., Xia, Y., Bex, V., & Midgley, P. M. (2014). Summary for Policymakers. In: Stocker, D. Qin, G. K. Plattner, M. Tignor, S. K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex, & P. M. Midgley (Eds.), Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (pp. 3-29). Cambridge, UK, and New York, NY, USA: Cambridge University Press. google scholar
- Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., ... & Knight, R. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457-463. google scholar
- Vadde, K. K., Feng, Q., Wang, J., McCarthy, A. J., & Sekar, R. (2019). Next-generation sequencing reveals fecal contamination and potentially pathogenic bacteria in a major inflow river of Taihu Lake. Environmental Pollution, 254, 113108. google scholar
- Van der Gucht, K., Cottenie, K., Muylaert, K., Vloemans, N., Cousin, S., Declerck, S., ... & De Meester, L. (2007). The power of species sorting: local factors drive bacterial community composition over a wide range of spatial scales. Proceedings of the National Academy of Sciences, 104(51), 20404-20409. google scholar
- Vaz-Moreira, I., Nunes, O. C., & Manaia, C. M. (2014). Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome. FEMS Microbiology Reviews, 38(4), 761-778. google scholar
- Vega, L., Jaimes, J., Morales, D., Martmez, D., Cruz-Saavedra, L., Munoz, M., & Ramfrez, J. D. (2021). Microbi-al Communities’ Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing. Microbial Ecology, 81, 847-863. google scholar
- Veilleux, H. D., Misutka, M. D., & Glover, C. N. (2021). Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring. Science of the Total Environment, 782, 146891. google scholar
- Vijayan, J., Nathan, V. K., Ammini, P., & Ammanamveetil, A. M. H. (2023). Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review. Environmental Science and Pollution Research, 1-24. google scholar
- Villena-Alemany, C., Mujakic, I., Porcal, P., Kobbzek, M., & Piwosz, K. (2023). Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake. Environmental Microbiology Reports, 15(1), 60-71. google scholar
- Wang, Y., Guo, M., Li, X., Liu, G., Hua, Y., Zhao, J., ... & Li, S. (2022). Shifts in microbial communities in shallow lakes depending on trophic states: Feasibility as an evaluation index for eutrophication. Ecological Indicators, 136, 108691. google scholar
- Wei, C., Sun, D., Yuan, W., Li, L., Dai, C., Chen, Z., Zeng, X., Wang, S., Zhang, Y., Jiang, S., Wu, Z., Liu, D., Jiang, L., & Peng, S. (2023). Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet. Environmental Research, 217, 114847. google scholar
- Yadav, A. N., Yadav, N., Kour, D., Kumar, A., Yadav, K., Kumar, A., ... & Saxena, A. K. (2019). Bacterial com-munity composition in lakes. In Freshwater Microbiology (pp. 1-71). Academic Press. google scholar
- Zhang, L., Cheng, Y., Gao, G., & Jiang, J. (2019). Spatial-temporal variation of bacterial communities in sedi-ments in Lake Chaohu, a large, shallow eutrophic lake in China. International Journal of Environmental Research and Public Health, 16(20), 3966. google scholar
- Zhong, M., Capo, E., Zhang, H., Hu, H., Wang, Z., Tian, W., ... & Bertilsson, S. (2023). Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China). Freshwater Biology, 68(1), 155-171. google scholar
- Zlatkovic, S., Medic, O., Predojevic, D., Nikolic, I., Subakov-Simic, G., Onjia, A., Beric, T., & Stankovic, S. (2022). Spatio-Temporal Dynamics in Physico-Chemical Properties, Phytoplankton and Bacterial Diversity as an Indication of the Bovan Reservoir Water Quality. Water, 14(3), 391. google scholar