Details

Title

Microbiome dynamics modeling and analysis in relation to spatio-temporal changes in physicochemical conditions of the water ecosystem

Journal title

Archives of Environmental Protection

Yearbook

2022

Volume

vol. 48

Issue

No 1

Affiliation

Woźnica, Andrzej : University of Silesia in Katowice, Faculty of Natural Sciences, Katowice, Poland ; Łozowski, Bartosz : University of Silesia in Katowice, Faculty of Natural Sciences, Katowice, Poland ; Absalon, Damian : University of Silesia in Katowice, Faculty of Natural Sciences, Katowice, Poland ; Krzyżowski, Michał : University of Silesia in Katowice, Faculty of Natural Sciences, Katowice, Poland ; Babczyńska, Agnieszka : University of Silesia in Katowice, Faculty of Natural Sciences, Katowice, Poland ; Kwaśniewski, Mirosław : Medical University of Bialystok, Faculty of Medicine, Bialystok, Poland ; Chwiałkowska, Karolina : Medical University of Bialystok, Faculty of Medicine, Bialystok, Poland ; Libera, Marcin : University of Silesia in Katowice, Faculty of Science and Technology, Katowice, Poland

Authors

Keywords

microbial communities ; water monitoring ; freshwater ecosystem ; metataxonomics

Divisions of PAS

Nauki Techniczne

Coverage

18-30

Publisher

Polish Academy of Sciences

Bibliography

  1. Absalon, D., Matysik, M., Woźnica, A., Łozowski, B., Jarosz, W., Ulańczyk, R., Babczyńska, A. & Pasierbiński, A. (2020). Multi-faceted environmental analysis to improve the quality of anthropogenic water reservoirs (Paprocany reservoir case study). Sensors (Switzerland), 20(9). DOI:10.3390/s20092626
  2. Andersen, M. S. (2007). An introductory note on the environmental economics of the circular economy. Sustainability Science, 2(1), 133–140. https://doi.org/10.1007/s11625-006-0013-6
  3. Anderson-Glenna, M. J., Bakkestuen, V. & Clipson, N. J. W. (2008). Spatial and temporal variability in epilithic biofilm bacterial communities along an upland river gradient. FEMS Microbiology Ecology, 64(3), 407–418. DOI:10.1111/j.1574-6941.2008.00480.x
  4. Aneja, K. (2008). A textbook of basic and applied microbiology. New Age International.
  5. Arora-Williams, K., Olesen, S. W., Scandella, B. P., Delwiche, K., Spencer, S. J., Myers, E. M., Abraham, S., Sooklal, A. & Preheim, S. P. (2018). Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake 06 Biological Sciences 0605 Microbiology 06 Biological Sciences 0602 Ecology 06 Biological Sciences 0604 Genetics. Microbiome, 6(1), 1–16. DOI:10.1186/s40168-018-0556-7
  6. Babczyńska, A., Tarnawska, M., Łaszczyca, P., Migula, P., Łozowski, B., Woźnica, A. & Augustyniak, M. (2021). Stress proteins concentration in caged Cyprinus carpioas a tool to monitor ecological stability in a model dam reservoir. Archives of Environmental Protection, 47(1), 101-116. DOI:10.24425/aep.2021.136452
  7. Beier, S., Witzel, K.-P. K.-P. & Marxsen, J. (2008). Bacterial community composition in Central European running waters examined by temperature gradient gel electrophoresis and sequence analysis of 16S rRNA genes. Applied and Environmental Microbiology, 74(1), 188–199. DOI:10.1128/AEM.00327-07
  8. Bibby, K., Viau, E. & Peccia, J. (2010). Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Water Research, 44(14), 4252–4260. DOI:10.1016/j.watres.2010.05.039
  9. Chao, A., Chiu, C.-H. & Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1558), 3599–3609. DOI:10.1098/rstb.2010.0272
  10. Chorus, I. & Bartram, J. (1999). Toxic Cyanobacteria in Water: A guide to their public health consequences, monitoring and management.
  11. Cottrell, M. T. & Kirchman, D. L. (2000). Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low-and high-molecular-weight dissolved organic matter. Applied and Environmental Microbiology, 66(4), 1692–1697.
  12. DeLong, E. F. (2005). Microbial community genomics in the ocean. Nature Reviews. Microbiology, 3(6), 459–469. DOI:10.1038/nrmicro1158
  13. DeLong, E. F. & Béjà, O. (2010). The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biology, 8(4), 1–5. DOI:10.1371/journal.pbio.1000359
  14. DeLong, E. F., Taylor, L. T., Marsh, T. L. & Preston, C. M. (1999). Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Applied and Environmental Microbiology, 65(12), 5554–5563.
  15. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P. & Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72(7), 5069–5072. DOI:10.1128/AEM.03006-05
  16. Eiler, A. & Bertilsson, S. (2004). Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environmental Microbiology, 6(12), 1228–1243. DOI:10.1111/j.1462-2920.2004.00657.x
  17. Falkowski, P. G., Fenchel, T. & Delong, E. F. (2008). The microbial engines that drive earth’s biogeochemical cycles. Science, 320(5879), 1034–1039. DOI:10.1126/science.1153213
  18. Fredricks, D. N. (2006). Introduction to the Rickettsiales and other intracellular prokaryotes. In The Prokaryotes (pp. 457–466). Springer.
  19. Fuhrman, J. a, Schwalbach, M. S. & Stingl, U. (2008). Proteorhodopsins: an array of physiological roles? Nature Reviews. Microbiology, 6(6), 488–494. DOI:10.1038/nrmicro1893
  20. Ghai, R., Hernandez, C. M., Picazo, A., Mizuno, C. M., Ininbergs, K., Díez, B., Valas, R., DuPont, C. L., McMahon, K. D., Camacho, A. & Rodriguez-Valera, F. (2012). Metagenomes of Mediterranean Coastal Lagoons. Scientific Reports, 2, 1–13. DOI:10.1038/srep00490
  21. Ghai, R., Rodŕíguez-Valera, F., McMahon, K. D., Toyama, D., Rinke, R., de Oliveira, T. C. S., Garcia, J. W., de Miranda, F. P. & Henrique-Silva, F. (2011). Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS ONE, 6(8). DOI:10.1371/journal.pone.0023785
  22. Glockner, F. O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A. & Amann, R. (2000). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Applied and Environmental Microbiology, 66(11), 5053–5065. DOI:10.1128/AEM.66.11.5053-5065.2000
  23. Gwiazda, R., Woźnica, A., Łozowski, B., Kostecki, M. & Flis, A. (2014). Impact of waterbirds on chemical and biological features of water and sediments of a large, shallow dam reservoir. Oceanological and Hydrobiological Studies, 43(4). DOI:10.2478/s13545-014-0160-9
  24. Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E., Methe, B., DeSantis, T. Z., Petrosino, J. F., Knight, R. & Birren, B. W. (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research, 21(3), 494–504. DOI:10.1101/gr.112730.110
  25. Hahn, M. W., Kasalicky, V., Jezbera, J., Brandt, U., Jezberova, J. & Simek, K. (2010). Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 60(6), 1358–1365. DOI:10.1099/ijs.0.013292-0
  26. Hahn, M. W., Kasalicky, V., Jezbera, J., Brandt, U. & Simek, K. (2010). Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 60(12), 2946–2950. DOI:10.1099/ijs.0.022384-0
  27. Hodges, B. & Dallimore, C. (2006). Estuary, Lake and Coastal Ocean Model: ELCOM v2. 2 Science Manual. Water, 62. DOI:10.1016/j.ecss.2007.05.033
  28. Jankowiak, J., Hattenrath-Lehmann, T., Kramer, B. J., Ladds, M. & Gobler, C. J. (2019). Deciphering the effects of nitrogen, phosphorus, and temperature on cyanobacterial bloom intensification, diversity, and toxicity in western Lake Erie. Limnology and Oceanography, 64(3), 1347–1370. DOI:10.1002/lno.11120
  29. Kasalicki, V., Jezbera, J., Simek, K., Hahn, M. W., Kasalicky, V., Jezbera, J., Simek, K. & Hahn, M. W. (2010). Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. International Journal of Systematic and Evolutionary Microbiology, 60(12), 2710–2714. DOI:10.1099/ijs.0.018952-0
  30. Kostecki, M. (2021). A new antrhropogenic lake Kuźnica Warężyńska: thermal and oxygen conditions after 14 years of exploitation in terms of protection and restoration. Archives of Environmental Protection, 47(2), 115-127. DOI:10.24425/aep.2021.137283
  31. Logares, R., Brate, J., Heinrich, F., Shalchian-Tabrizi, K., Bertilsson, S., Brte, J., Heinrich, F., Shalchian-Tabrizi, K. & Bertilsson, S. (2010). Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Molecular Biology and Evolution, 27(2), 347–357. DOI:10.1093/molbev/msp239
  32. Malmstrom, R. R., Kiene, R. P., Vila, M. & Kirchman, D. L. (2005). Dimethylsulfoniopropionate (DMSP) assimilation by Synechococcus in the Gulf of Mexico and northwest Atlantic Ocean. Limnology and Oceanography, 50(6), 1924–1931. DOI:10.4319/lo.2005.50.6.1924
  33. Matysik, M., Absalon, D., Habel, M. & Maerker, M. (2020). Surface water quality analysis using CORINE data: An application to assess reservoirs in Poland. Remote Sensing, 12(6), 16–20. DOI:10.3390/rs12060979
  34. Mendez-Garcia, C., Pelaez, A. I., Mesa, V., Sánchez, J., Golyshina, O. V. & Ferrer, M. (2015). Microbial diversity and metabolic networks in acid mine drainage habitats. Frontiers in Microbiology, 6(475). DOI:10.3389/fmicb.2015.00475
  35. Miller, S. R., Strong, A. L., Jones, K. L. & Ungerer, M. C. (2009). Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Applied and Environmental Microbiology, 75(13), 4565–4572. DOI:10.1128/AEM.02792-08
  36. Percent, S. F., Frischer, M. E., Vescio, P. A., Duffy, E. B., Milano, V., McLellan, M., Stevens, B. M., Boylen, C. W. & Nierzwicki-Bauer, S. A. (2008). Bacterial community structure of acid-impacted lakes: What controls diversity? Applied and Environmental Microbiology, 74(6), 1856–1868. DOI:10.1128/AEM.01719-07
  37. Pernthalerlr, J., Sattlerl, B., Simek, K., Schwarzenbacherl, A., Psennerl, R., Pernthaler, J., Sattler, B., Šimek, K., Schwarzenbacher, A. & Psenner, R. (1996). Top-down effects on the size-biomass distribution of a freshwater bacterioplankton community. Aquatic Microbial Ecology, 10(3), 255–263. DOI:10.3354/ame010255
  38. Salcher, M. M., Pernthaler, J. & Posch, T. (2011). Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria “that rule the waves” (LD12). The ISME Journal, 5(8), 1242–1252. DOI:10.1038/ismej.2011.8
  39. Sekar, R., Pernthaler, A., Pernthaler, J., Posch, T., Amann, R. & Warnecke, F. (2003). An Improved Protocol for Quantification of Freshwater Actinobacteria by Fluorescence In Situ Hybridization An Improved Protocol for Quantification of Freshwater Actinobacteria by Fluorescence In Situ Hybridization. Applied and Environmental Microbiology, 69(5), 2928–2935. DOI10.1128/AEM.69.5.2928
  40. Smith, V. H., Joye, S. B. & Howarth, R. W. (2006). Eutrophication of freshwater and marine ecosystems. Limnol. Oceanogr., 51(1, part 2), 351–355. DOI:10.4319/lo.2006.51.1_part_2.0351
  41. Stanimirova, I., Woznica, A., Plociniczak, T., Kwasniewski, M. & Karczewski, J. (2016). A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data. Talanta, 160, 148–156. DOI:10.1016/j.talanta.2016.07.006
  42. Thatoi, H., Behera, B. C., Mishra, R. R. & Dutta, S. K. (2013). Biodiversity and biotechnological potential of microorganisms from mangrove ecosystems: A review. Annals of Microbiology, 63(1), 1–19. DOI:10.1007/s13213-012-0442-7
  43. USEPA. (2006). Method 1680: Fecal Coliforms in Sewage Sludge (Biosolids) by Multiple-Tube Fermentation using Lauryl Tryptose Broth (LTB) and EC Medium. USEPA.
  44. Vaishnava, S., Yamamoto, M., Severson, K. M., Ruhn, K. a, Yu, X., Koren, O., Ley, R., Wakeland, E. K. & Hooper, L. V. (2011). The Antibacterial Lectin RegIII. Science, 334(October), 255–258.
  45. Vila-Costa, M., Simo, R., Harada, H., Gasol, J. M., Slezak, D., Kiene, R. P., Simó, R., Harada, H., Gasol, J. M., Slezak, D. & Kiene, R. P. (2006). Dimethylsulfoniopropionate uptake by marine phytoplankton. Science (New York, N.Y.), 314(5799), 652–654. DOI:10.1126/science.1131043
  46. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16), 5261–5267. DOI:10.1128/AEM.00062-07
  47. Warnecke, F., Amann, R. & Pernthaler, J. (2004). Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environmental Microbiology, 6(3), 242–253. DOI:10.1111/j.1462-2920.2004.00561.x
  48. Woznica, A., Nowak, A., Ziemski, P., Kwasniewski, M. & Bernas, T. (2013). Stimulatory Effect of Xenobiotics on Oxidative Electron Transport of Chemolithotrophic Nitrifying Bacteria Used as Biosensing Element. PLoS ONE, 8(1). DOI:10.1371/journal.pone.0053484
  49. Zeng, Y., Kasalický, V., Šimek, K., Koblízek, M., Kasalicky, V., Simek, K. & Koblizek, M. (2012). Genome sequences of two freshwater betaproteobacterial isolates, limnohabitans species strains Rim28 and Rim47, indicate their capabilities as both photoautotrophs and ammonia oxidizers. Journal of Bacteriology, 194(22), 6302–6303. DOI:10.1128/JB.01481-12
  50. Zwart, G., Crump, B. C., Kamst-van Agterveld, M. P., Hagen, F. & Han, S. K. (2002). Typical freshwater bacteria: An analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquatic Microbial Ecology, 28(2), 141–155. DOI:10.3354/ame028141

Date

7.03.2022

Type

Article

Identifier

DOI: 10.24425/aep.2022.140542

Abstracting & Indexing

Abstracting & Indexing


Archives of Environmental Protection is covered by the following services:


AGRICOLA (National Agricultural Library)

Arianta

Baidu

BazTech

BIOSIS Citation Index

CABI

CAS

DOAJ

EBSCO

Engineering Village

GeoRef

Google Scholar

Index Copernicus

Journal Citation Reports™

Journal TOCs

KESLI-NDSL

Naviga

ProQuest

SCOPUS

Reaxys

Ulrich's Periodicals Directory

WorldCat

Web of Science

×