Vertical Stratification of Archaeal Communities in Lake Sediments: A Comparative Analysis of Dead and Thriving Lakes
Abstract:
Archaea are influenced by environmental conditions in various ecosystems and are essential to global biogeochemical cycles. By contrasting healthy and dead lakes, this study examines the vertical stratification of archaeal populations in lake sediments. Archaea play a role in the breakdown of organic matter, the oxidation of ammonia, and the formation of methane. The study investigates the effects of temperature variations, nutrition availability, redox conditions, and oxygen gradients on archaeal diversity and distribution. The study highlights the importance of archaea in preserving ecosystem health, especially in sedimentary contexts, using DNA sequencing, community analysis, and environmental characterization. The results demonstrate that although dead lakes, which are defined by oxygen depletion and changed redox gradients, show decreased diversity and ecological services, healthy lakes sustain a variety of archaeal populations. Gaining knowledge of these microbial communities can help us better understand how resilient aquatic ecosystems are to environmental stresses like eutrophication and climate change, as well as the potential for ecological restoration. The study emphasizes how crucial archaea are to preserving the health of ecosystems and how their dispersion affects the maintenance of aquatic environments.
KeyWords:
Archaeal communities, Sediment stratification, Biogeochemical cycles, Ecosystem resilience
References:
1. Andrei, A. Ş., Robeson, M. S., Baricz, A., Coman, C., Muntean, V., Ionescu, A., Etiope, G., Alexe, M., Sicora, C. I., Podar, M., & Banciu, H. L. (2015). Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes. ISME Journal, 9(12), 2642–2656. https://doi.org/10.1038/ismej.2015.60
2. Baldrian, P. (2017). Forest microbiome: Diversity, complexity and dynamics. FEMS Microbiology Reviews, 41(2), 109–130. https://doi.org/10.1093/femsre/fuw040
3. Bhaduri, D., Sihi, D., Bhowmik, A., Verma, B. C., Munda, S., & Dari, B. (2022). A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Frontiers in Microbiology, 13.
https://doi.org/10.3389/fmicb.2022.938481
4. Bräsen, C., Esser, D., Rauch, B., & Siebers, B. (2014). Carbohydrate metabolism in archaea: Current insights into unusual enzymes and pathways and their regulation. JAMA Ophthalmology, 132(3), 326–331.
https://doi.org/10.1128/MMBR.00041-13
5. Cadena, S., Aguirre-Macedo, M. L., Cerqueda-García, D., Cervantes, F. J., Herrera-Silveira, J. A., & García-Maldonado, J. Q. (2019). Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico. Estuarine, Coastal and Shelf Science, 230(October). https://doi.org/10.1016/j.ecss.2019.106433
6. Cavicchioli, R. (2011). Archaea—timeline of the third domain. Nature Reviews Microbiology, 9(1), 51–61.
7. Chen, Y., Qiu, K., Zhong, Z., & Zhou, T. (2021). Influence of Environmental Factors on the Variability of Archaeal Communities in a Karst Wetland. Frontiers in Microbiology, 12(September), 1–16.
https://doi.org/10.3389/fmicb.2021.675665
8. Fan, X., & Xing, P. (2016). Differences in the composition of archaeal communities in sediments from contrasting zones of Lake Taihu. Frontiers in Microbiology, 7(SEP), 1–11. https://doi.org/10.3389/fmicb.2016.01510
9. Fenchel, T., & Finlay, B. (2008). Oxygen and the spatial structure of microbial communities. Biological Reviews, 83(4), 553–569. https://doi.org/10.1111/j.1469-185X.2008.00054.x
10. Gerphagnon, M., Macarthur, D. J., Latour, D., Gachon, C. M. M., Van Ogtrop, F., Gleason, F. H., & Sime-Ngando, T. (2015). Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism. Environmental Microbiology, 17(8), 2573–2587. https://doi.org/10.1111/1462-2920.12860
11. Ghai, R., Pašić, L., Fernández, A. B., Martin-Cuadrado, A. B., Mizuno, C. M., McMahon, K. D., Papke, R. T., Stepanauskas, R., Rodriguez-Brito, B., Rohwer, F., Sánchez-Porro, C., Ventosa, A., & Rodríguez-Valera, F. (2011). New abundant microbial groups in aquatic hypersaline environments. Scientific Reports, 1, 135. https://doi.org/10.1038/srep00135
12. Hess, S. S., Burns, D. A., Boudinot, F. G., Brown-Lima, C., Corwin, J., Foppert, J. D., Robinson, G. R., Rose, K. C., Schlesinger, M. D., Shuford, R. L., & others. (2024). New York State Climate Impacts Assessment Chapter 05: Ecosystems.
13. Huang, Q. H., Wang, Z. J., Wang, D. H., Wang, C. X., Ma, M., & Jin, X. C. (2005). Origins and mobility of phosphorus forms in the sediments of Lakes Taihu and Chaohu, China. Journal of Environmental Science and Health - Part A Toxic/Hazardous Substances and Environmental Engineering, 40(1), 91–102. https://doi.org/10.1081/ESE-200033593
14. Jenny, J. P., Normandeau, A., Francus, P., Taranu, Z. E., Gregory-Eaves, I., Lapointe, F., Jautzy, J., Ojala, A. E. K., Dorioz, J. M., Schimmelmann, A., & Zolitschkal, B. (2016). Urban point sources of nutrients were the leading cause for the historical spread of hypoxia across European lakes. Proceedings of the National Academy of Sciences of the United States of America, 113(45), 12655–12660. https://doi.org/10.1073/pnas.1605480113
15. Jiang, H., Dong, H., Yu, B., Liu, X., Li, Y., Ji, S., & Zhang, C. L. (2007). Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environmental Microbiology, 9(10), 2603–2621.
16. Jiang, Z., Huang, Q., Cui, K., Deng, G., Huang, Y., Yu, K., Li, C.-X., & Chen, Y. (2024). Differential insights into the distribution characteristics of archaeal communities and their response to typical pollutants in the sediments and soils of deep-water reservoir. Journal of Environmental Chemical Engineering, 12(6), 114256.
17. Jørgensen, B. B., & Boetius, A. (2007). Feast and famine - Microbial life in the deep-sea bed. Nature Reviews Microbiology, 5(10), 770–781. https://doi.org/10.1038/nrmicro1745
18. Kassim, M., Hashim, N., & Yusof, N. (2017). Archaea Domain as Biocatalyst in Environmental Biotechnology and Industrial Applications: A Review. Journal of Advances in Microbiology, 5(2), 1–21. https://doi.org/10.9734/jamb/2017/35591
19. Katayama, T., Yoshioka, H., Kaneko, M., Amo, M., Fujii, T., Takahashi, H. A., Yoshida, S., & Sakata, S. (2022). Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site. ISME Journal, 16(5), 1464–1472. https://doi.org/10.1038/s41396-021-01175-7
20. Kimble, J. C., Winter, A. S., Spilde, M. N., Sinsabaugh, R. L., & Northup, D. E. (2018). A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA. FEMS Microbiology Ecology, 94(11), 1–17. https://doi.org/10.1093/FEMSEC/FIY173
21. Lan, J., Liu, P., Hu, X., & Zhu, S. (2024). Harmful Algal Blooms in Eutrophic Marine Environments: Causes, Monitoring, and Treatment. Water (Switzerland), 16(17), 1–64. https://doi.org/10.3390/w16172525
22. Li, Q., Wang, F., Chen, Z., Yin, X., & Xiao, X. (2012). Stratified active archaeal communities in the sediments of Jiulong River estuary, China. Frontiers in Microbiology, 3(AUG). https://doi.org/10.3389/fmicb.2012.00311
23. Lyu, Z., Shao, N., Akinyemi, T., & Whitman, W. B. (2018). Methanogenesis. Current Biology, 28(13), R727–R732. https://doi.org/10.1016/j.cub.2018.05.021
24. Marakushev, S. A., & Belonogova, O. V. (2018). Development of nascent autotrophic carbon fixation systems in various redox conditions of the fluid degassing in early Earth. Biogeosciences Discussions, 1–19. https://doi.org/10.5194/bg-2018-291
25. Meng, J., Xu, J., Qin, D., He, Y., Xiao, X., & Wang, F. (2014). Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. The ISME Journal, 8(3), 650–659.
26. Moore, E. K., Jelen, B. I., Giovannelli, D., Raanan, H., & Falkowski, P. G. (2017). Metal availability and the expanding network of microbial metabolisms in the Archaean eon. Nature Geoscience, 10(9), 629–636. https://doi.org/10.1038/ngeo3006
27. Morris, B. E. L., Henneberger, R., Huber, H., & Moissl-Eichinger, C. (2013). Microbial syntrophy: Interaction for the common good. FEMS Microbiology Reviews, 37(3), 384–406. https://doi.org/10.1111/1574-6976.12019
28. Morrison, J. M., Baker, K. D., Zamor, R. M., Nikolai, S., Elshahed, M. S., & Youssef, N. H. (2017). Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS ONE, 12(5). https://doi.org/10.1371/journal.pone.0177488
29. Nazir, R., Rehman, S., Nisa, M., & Baba, U. ali. (2019). Exploring bacterial diversity: From cell to sequence. In Freshwater Microbiology: Perspectives of Bacterial Dynamics in Lake Ecosystems. Elsevier Inc. https://doi.org/10.1016/B978-0-12-817495-1.00007-4
30. Offre, P., Spang, A., & Schleper, C. (2013). Archaea in biogeochemical cycles. Annual Review of Microbiology, 67(May), 437–457. https://doi.org/10.1146/annurev-micro-092412-155614
31. Pester, M., Schleper, C., & Wagner, M. (2011). The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology, 14(3), 300–306.
32. Pichler, H., & Emmerstorfer-Augustin, A. (2018). Modification of membrane lipid compositions in single-celled organisms--From basics to applications. Methods, 147, 50–65.
33. Rissanen, A. J., Peura, S., Mpamah, P. A., Taipale, S., Tiirola, M., Biasi, C., Mäki, A., & Nykänen, H. (2019). Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake. FEMS Microbiology Letters, 366(5), 1–11. https://doi.org/10.1093/femsle/fnz044
34. Rodrigues, T., Catão, E., Bustamante, M. M. C., Quirino, B. F., Kruger, R. H., & Kyaw, C. M. (2014). Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna. Archaea, 2014. https://doi.org/10.1155/2014/957145
35. Ruuskanen, M. O., St. Pierre, K. A., St. Louis, V. L., Aris-Brosou, S., & Poulain, A. J. (2018). Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada. Frontiers in Microbiology, 9(JUN), 1–16. https://doi.org/10.3389/fmicb.2018.01138
36. Santoro, A. E. (2010). Cycle microbiologique de l’azote à l’interface eau salée - eau douce. Hydrogeology Journal, 18(1), 187–202. https://doi.org/10.1007/s10040-009-0526-z
37. Schwefel, R., Steinsberger, T., Bouffard, D., Bryant, L. D., Müller, B., & Wüest, A. (2018). Using small-scale measurements to estimate hypolimnetic oxygen depletion in a deep lake. Limnology and Oceanography, 63, S54–S67. https://doi.org/10.1002/lno.10723
38. Shaibu, S. E., Adekola, F. A., Adegoke, H. I., & Abdus-Salam, N. (2015). Heavy metal speciation patterns of selected dumpsites in Ilorin Metropolis. International Journal of Chemical, Material and Environmental Research, 2(1), 1-11.
39. Shaibu, S. E., Effiom, A. O., Essien, N. S., Archibong, E. S., Iboutenang, N. D., Effiong, A. I., ... & Eyo, G. A. (2024). Evaluating Groundwater Safety: Heavy Metal Contamination of Selected Boreholes across Uyo Metropolis, Akwa Ibom State, Nigeria. UMYU Journal of Microbiology Research, 9(3), 267-277.
40. Somayaji, A., Dhanjal, C. R., Lingamsetty, R., Vinayagam, R., Selvaraj, R., Varadavenkatesan, T., & Govarthanan, M. (2022). An insight into the mechanisms of homeostasis in extremophiles. Microbiological Research, 263, 127115.
41. Tang, C., Madigan, M. T., & Lanoil, B. (2013). Bacterial and archaeal diversity in sediments of west lake bonney, mcmurdo dry valleys, antarctica. Applied and Environmental Microbiology, 79(3), 1034–1038. https://doi.org/10.1128/AEM.02336-12
42. Tardy, V., Etienne, D., Masclaux, H., Essert, V., Millet, L., Verneaux, V., & Lyautey, E. (2021). Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia – a biogeographical study on Lake Remoray (France). FEMS Microbiology Ecology, 97(10). https://doi.org/10.1093/femsec/fiab126
43. Thakur, T. K., Barya, M. P., Dutta, J., Mukherjee, P., Thakur, A., Swamy, S. L., & Anderson, J. T. (2023). Integrated Phytobial Remediation of Dissolved Pollutants from Domestic Wastewater through Constructed Wetlands: An Interactive Macrophyte-Microbe-Based Green and Low-Cost Decontamination Technology with Prospective Resource Recovery. Water (Switzerland), 15(22). https://doi.org/10.3390/w15223877
44. Uchman, A., & Wetzel, A. (2011). Deep-sea ichnology: The relationships between depositional environment and endobenthic organisms. In Developments in Sedimentology (1st ed., Vol. 63, Issue C). Heiko Hneke and Thierry Mulder. https://doi.org/10.1016/B978-0-444-53000-4.00008-1
45. UdoUSoro, I. I., Umoren, I. U., Izuagie, J. M., Ikpo, C. U., Ngeri, S. F., & Shaibu, E. S. (2015). Soil invertebrates as bio-monitors of toxic metals pollution in impacted soils. Current World Environment, 10(2), 367.
46. Ventosa, A., de la Haba, R. R., Sánchez-Porro, C., & Papke, R. T. (2015). Microbial diversity of hypersaline environments: a metagenomic approach. Current Opinion in Microbiology, 25(June), 80–87. https://doi.org/10.1016/j.mib.2015.05.002
47. Vuillemin, A., Coolen, M. J. L., Kallmeyer, J., Liebner, S., Barouillet, C., & Publishing, S. I. (2023). Page | 1.
48. Wahab, A., Muhammad, M., Munir, A., Abdi, G., Zaman, W., Ayaz, A., Khizar, C., & Reddy, S. P. P. (2023). Role of arbuscular mycorrhizal fungi in regulating growth, enhancing productivity, and potentially influencing ecosystems under abiotic and biotic stresses. Plants, 12(17), 3102.
49. Wallenius, A. J., Dalcin Martins, P., Slomp, C. P., & Jetten, M. S. M. (2021). Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments. Frontiers in Microbiology, 12(February). https://doi.org/10.3389/fmicb.2021.631621
50. Wan, W., Grossart, H.-P., Zhang, W., Xiong, X., Yuan, W., Liu, W., & Yang, Y. (2024). Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria. Water Research, 267, 122516.
51. Wurzbacher, C., Fuchs, A., Attermeyer, K., Frindte, K., Grossart, H. P., Hupfer, M., Casper, P., & Monaghan, M. T. (2017). Shifts among eukaryota, bacteria, and archaea define the vertical organization of a lake sediment. Microbiome, 5(1), 1–16. https://doi.org/10.1186/S40168-017-0255-9
52. Xiao, K. Q., Beulig, F., Kjeldsen, K. U., Jørgensen, B. B., & Risgaard-Petersen, N. (2017). Concurrent methane production and oxidation in surface sediment from Aarhus Bay, Denmark. Frontiers in Microbiology, 8(JUN), 1–12. https://doi.org/10.3389/fmicb.2017.01198
53. Xiong, W., Xie, P., Wang, S., Niu, Y., Yang, X., & Chen, W. (2015). Sources of organic matter affect depth-related microbial community composition in sediments of Lake Erhai, Southwest China. Journal of Limnology, 74(2), 310–323. https://doi.org/10.4081/jlimnol.2014.1106
54. Yang, Y., Dai, Y., Wu, Z., Xie, S., & Liu, Y. (2016). Temporal and spatial dynamics of archaeal communities in two freshwater lakes at different trophic status. Frontiers in Microbiology, 7(MAR), 1–14.
https://doi.org/10.3389/fmicb.2016.00451
55. Zhalnina, K., Dörr de Quadros, P., Camargo, F. A. O., & Triplett, E. W. (2012). Drivers of archaeal ammonia-oxidizing communities in soil. Frontiers in Microbiology, 3(JUN), 1–9. https://doi.org/10.3389/fmicb.2012.00210
56. Zhang, Z. bin, Tan, X. bo, Wei, L. lei, Yu, S. miao, & Wu, D. ji. (2012). Comparison between the lower Nansi Lake and its inflow rivers in sedimentary phosphorus fractions and phosphorus adsorption characteristics. Environmental Earth Sciences, 66(5), 1569–1576. https://doi.org/10.1007/s12665-011-1400-6
57. Zhang, J., Yang, Y., Zhao, L., Li, Y., Xie, S., & Liu, Y. (2015). Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Applied Microbiology and Biotechnology, 99(7), 3291–3302. https://doi.org/10.1007/s00253-014-6262-x
58. Zhang, L., Zhao, T., Shen, T., & Gao, G. (2019). Seasonal and spatial variation in the sediment bacterial community and diversity of Lake Bosten, China. Journal of Basic Microbiology, 59(2), 224–233. https://doi.org/10.1002/jobm.201800452
59. Zhang, Y., Shen, J., He, L., Feng, J., Chi, L., & Wang, X. (2024). Challenge to Lake Ecosystems: Changes in Thermal Structure Triggered by Climate Change. Water (Switzerland), 16(6). https://doi.org/10.3390/w16060888
60. Zhao, R., Mogollón, J. M., Roerdink, D. L., Thorseth, I. H., Økland, I., & Jørgensen, S. L. (2021). Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments. ISME Journal, 15(12), 3657–3667. https://doi.org/10.1038/s41396-021-01041-6
61. Zhou, Z., Meng, H., Liu, Y., Gu, J. D., & Li, M. (2017). Stratified bacterial and archaeal community in mangrove and intertidal wetland mudflats revealed by high throughput 16S rRNA gene sequencing. Frontiers in Microbiology, 8(NOV), 1–19. https://doi.org/10.3389/fmicb.2017.02148
62. Zou, D., Liu, H., & Li, M. (2020). Community, Distribution, and Ecological Roles of Estuarine Archaea. Frontiers in Microbiology, 11(August), 1–18. https://doi.org/10.3389/fmicb.2020.02060
63. Zou, D., Qi, Y., & Zhou, J. (2025). Unveiling the life of archaea in sediments : Diversity , metabolic potentials , and ecological roles. August 2024, 1–17. https://doi.org/10.1002/imo2.56