Changes in the bacterial community composition of different habitats along a polluted river (Suquía River, Cordoba, Argentina)

Authors

  • Carolina Merlo Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba. Instituto Multidisciplinario de Biología Vegetal (IMBiV-CONICET).
  • María V. Amé CIBICI, Departamento de Bioquímica Clínica-Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba.
  • Lidwina Bertrand CIBICI, Departamento de Bioquímica Clínica-Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba.
  • Adriana Abril Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba.

DOI:

https://doi.org/10.25260/EA.17.27.1.0.401

Abstract

The objective of the present study was to investigate the influence of environmental conditions on the bacterial community composition in water, sediment and riparian soil during different water flow periods. For this purpose, samples of three habitats (water, sediment and riparian soil) were collected from five polluted sites and one reference site along the Suquía River during high and low water flow periods. The pH, dissolved oxygen, conductivity and water temperature were measured "in situ", with total organic carbon content, nitrate and ammonia concentration being evaluated for all samples. In addition, pH, conductivity and total N were determined in the sediment and riparian soil samples, and the bacterial community composition of water, sediments and riparian soil samples was monitored using restriction fragment length polymorphism of the 16S rRNA gene. The results showed that the bacterial community composition of water was different from that of sediments or riparian soil. A redundancy analysis indicated that the changes in the bacterial community composition in the Suquía River were primarily correlated with variations in dissolved oxygen, conductivity and pH. The water bacterial community composition was very variable among sites and water flow periods, while that of sediments differed according to the water flow period, which was associated with temperature variation. Lastly, in riparian soil, differences were found in the bacterial community composition of the sites located before and after Cordoba city. Our findings suggest distinct distribution patterns in the bacterial community compositions of the three habitats evaluated.

References

Allison, S. D., and J. B. H. Martiny. 2008. Resistance, resilience, and redundancy in microbial communities. P Natl Acad Sci USA 105:11512-11519.

Amaral, V., D. Graeber, D. Calliari, and C. Alonso. 2016. Strong linkages between DOM optical properties and main clades of aquatic bacteria. Limnol Oceanogr 61:906-918.

Amé, M. V., M. D. Díaz, and D. A. Wunderlin. 2003. Occurrence of toxic cyanobacterial blooms in San Roque Reservoir (Córdoba, Argentina): a field and chemometric study. Environ Toxicol 18:192-201.

Arroyo, P., L. E. Sáenz de Miera, and G. Ansola. 2015. Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands. Sci Total Environ 506-507:380-390.

Bai, Y., Q. Shi, D. Wen, Z. Li, W. A. Jefferson, C. Feng, and X. Tang. 2012. Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China. Plos One 7:1-10.

Balzarini, M. G., and J. A. Di Rienzo. 2013. InfoGen FCA, Universidad Nacional de Córdoba, Argentina. http://www.info-gen.com.ar.

Bartram, A. K., J. Xingpeng, M. D. J. Lynch, A. P. Masella, G. W. Nicol, J. Dushoff, and J. D. Neufeld. 2014. Exploring links between pH and bacterial community composition in soils from the Craibstone Exper- imental Farm. FEMS Microbiol Ecol 87:403-15.

Barton, L. L., and D. E. Northup. 2011. Microbial Ecology. Wiley-Blackwell, New Jersey, USA.

Bissett, A., C. Burke, P. L. M. Cook, and J. P. Bowman. 2007. Bacterial community shifts in organically perturbed sediments. Environ Microbiol 9:46-60.

Borcard, D., F. Gillet, and P. Legendre. 2011. Numerical Ecology whit R. Springer-Verlag, New York, USA.

Carey, R. O., and K. W. Migliaccio. 2009. Contribution of wastewater treatment plant effluents to nutrient dynamics in aquatic systems: a review. Environ Manage 44:205-217.

Chen, Z., Z. Zhou, and X. Peng. 2013. Effects of wet and dry seasons on the aquatic bacterial community structure of the Three Gorges Reservoir. World J Microbiol Biotechnol 29:841-853.

Comte, J., P. A. del Giorgio. 2010. Linking the patterns of change in composition and function in bacterioplankton successions along environmental gradients. Ecology 91:1466-1476.

Di Rienzo, J. A., F. Casanoves, M. G, Balzarini, L. González, M. Tablada, and C. W. Robledo. 2013. InfoStat, FCA, Universidad Nacional de Córdoba, Argentina. http://www.infostat.com.ar.

Dillon, J. G., L. M. McMath, and A. L. Trout. 2009. Seasonal changes in bacterial diversity in the Salton Sea. Hydrobiologia 632:49-64.

Duarte, S., C. Pascoal, and F. Cássio. 2008. High diversity of fungi may mitigate the impact of pollution on plant litter decomposition in streams. Microb Ecol 56:688-695.

Febria, C. M., R. R. Fulthorpe, and D. D. Williams. 2010. Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments. Hydrobiologia 647:113-126.

Fujii, M., H. Kojima, T. Iwata, J. Urabe, and M. Fukui. 2012. Dissolved organic carbon as major environmental factor affecting bacterioplankton communities in mountain lakes of eastern Japan. Microb Ecol 63:496-508.

Galanti, L. N., M. V. Amé, and D. A. Wunderlin. 2013. Accumulation and detoxification dynamic of cyanotoxins in the freshwater shrimp Palaemonetes argentinus. Harmful Algae 27:88-97.

Gao, Y. C., J. N. Wang, S. H. Guo, Y. L. Hu, T. T. Li, R. M. D. H. Zeng. 2015. Effects of salinization and crude oil contamination on soil bacterial community structure in the Yellow River Delta region, China. Appl Soil Ecol 86:165-173.

Haack, S. K., L. R. Fogarty, T. G. West, E. W. Alm, J. T. McGuire, D. T. Long, D. W. Hyndman, and L. J. Forney. 2004. Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer. Environ Microbiol 6:438-448.

Ibekwe, A. M., M. B. Leddy, R. M. Bold, and A. K. Graves. 2012. Bacterial community composition in low-flowing river water with different sources of pollutants. FEMS Microbiol Ecol 79:155-166.

Ibekwe, A. M., J. Ma, and S. E. Murinda. 2016. Bacterial community composition and structure in an Urban River impacted by different pollutant sources. Sci Total Environm 566-567:1176-1185.

Ikenaga, M., R. Guevara, A. L. Dean, C. Pisani, and J. N. Boyer. 2010. Changes in community structure of sediment bacteria along the Florida coastal everglades marsh-mangrove-seagrass salinity gradient. Microb Ecol 59:284-95.

Judd, K. E., B. C. Crump, and G. W. Kling. 2006. Variation in dissolved organic matter controls bacterial production and community composition. Ecology 87:2068-2079.

Jayakumar, A., G. D. O’Mullan, S. W. A. Naqvi, and B. B. Ward. 2009. Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones. Microb Ecol 58:350-362.

Kara, E. L., P. C. Hanson, Y. Hen Hu, L. Winslow, and K. D. McMahon. 2013. A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA. The ISME Journal 7:680-684.

Keeney, D., and D. Nelson. 1982. Nitrogen inorganic forms. Pp. 643-698 in: A. L. Page, R. Miller and D. Keeney (eds.). Methods of Soil Analysis Vol 2. Chemical and Microbiological Properties. American Society of Agronomy and Soil Science, Madison, WI, USA.

Kimura, M., T. Shibagaki, Y. Nakajima, K. Matsuya, and M. Ikenaga. 2002. Community structure of the microbiota in the floodwater of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analyses. Biol Fert Soils 36:306-312.

Kirchman, D. L., R. R. Malmstrom, and M. T. Cottrell. 2005. Control of bacterial growth by temperature and organic matter in the Western Arctic. Deep-Sea Res PT II 52:3386-3395.

Klute, A. 1986. Methods of Soil Analysis. Vol 1. Physical and Mineralogical Methods. American Society of Agronomy and Soil Science, Madison, WI, USA.

Lane, D. J. 1991. 16S/23S rRNA sequencing. Pp. 115-149 in: E. Stackebrandt and M. Goodfellow (eds.). Nucleic acid techniques in bacterial systematics. Wiley, New York, New York, USA.

Legendre, P., and E. D. Gallagher. 2001. Ecologically meaningful transformations for ordination of species data. Oecologia 129:271-280.

Lennon, J. T., and S. E. Jones. 2011. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9:119-130.

Ligi, T., K. Oopkaup, M. Truu, J. K. Preem, H. Nõlvak. W. J. Mitsch, Ü. Mander, and J. Truu. 2014. Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing. Ecological Engineering 72:56-66.

Merlo, C., A. Abril, M. V. Amé, G. A. Argüello, H. A. Carreras, M. S. Chiappero, A. C. Hued, E. Wannaz, L. N. Galanti, M. V. Monferrán, C. M. González, and V. M. Solís. 2011. Integral assessment of pollution in the Suquía River (Córdoba, Argentina) as a contribution to lotic ecosystem restoration programs. Sci Total Environ 409:5034-5045.

Merlo, C., and A. Abril. 2014a. Multidisciplinary approach to assess the water self-depuration characteristics of Suquía River (Córdoba, Argentina). Rev Chil Hist Nat 87:1-12.

Merlo, C., L. Reyna, A. Abril, M. V. Amé, and S. Genti-Raimondi. 2014b. Environmental factors associated with heterotrophic nitrogen-fixing bacteria in water, sediment and riparian soil of Suquía River. Limnologica 48:71-79.

Mulvaney, R. L. 1996. Nitrogen-inorganic forms. Pp. 1123-1184 in: D. L. Sparks, A. L. Page, P. A. Helmke, R. H. Loeppert, P. N. Soltanpour, M. A. Tabatabai, C. T. Johnston and M. E. Sumner (eds.). Methods of soil analysis, Part 3: Chemical methods. Soil Science Society of America, Inc, American Society of Agronomy, Inc, Madison, USA.

Nelson, D. W., and L. E. Sommers. 1996. Total Carbon, organic carbon, and organic matter. Pp. 961-1010 in: D. L. Sparks, A. L. Page, P. A. Helmke, R. H. Loeppert, P. N. Soltanpour, M. A. Tabatabai, C. T. Johnston and M. E. Sumner (eds.). Methods of Soil Analysis, Part 3: Chemical methods. Soil Science Society of America, Inc, American Society of Agronomy, Inc, Madison, USA.

Odum, E. P. 2003. Ecología. McGraw Hill Interamericana, México.

Pasquini, A. I., S. M. Formica, and G. A. Sacchi. 2012. Hydrochemistry and nutrients dynamic in the Suquía River urban catchment's Córdoba, Argentina. Environ Earth Sci 65:453-467.

Paul, E. 2007. Soil Microbiology, Ecology and Biochemistry. Academic Press, Inc, San Diego, USA.

Porat, I., T. A. Vishnivetskaya, J. J Mosher, C. C. Brandt, Z. K. Yang, S. C. Brooks, L. Liang, M. M. Drake, M. Podar, S. D. Brown, and A. V. Palumbo. 2010. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol 60:784-795.

Powell, S. M., J. P. Bowman, I. Snape, and J. S. Stark. 2003. Microbial community variation in pristine and polluted near shore Antarctic sediments. FEMS Microbiol Ecol 45:135-145.

Ramírez Moreno, S., S. Méndez-Álvarez, M. Martínez-Alonso, I. Esteve, and N. Gaju. 2004. Factors affecting interpretation of restriction fragment length polymorphism (RFLP) patterns from PCR-amplified bacterial 16S rRNA genes: operon number and primer mismatching. Curr Microbiol 48:285-290.

Ramírez Moreno, S., M. Martínez-Alonso, S. Méndez-Álvarez, and N. Gaju. 2005. Seasonal microbial ribotype shifts in the sulfurous karstic lakes Cisó and Vilar, in northeastern Spain. Int Microbiol 8:235-242.

Reyna, L., D. A. Wunderlin, and S. Genti-Raimondi. 2010. Identification and quantification of a novel nitrate-reducing community in sediments of Suquía River along a nitrate gradient. Environ Pollut 158:1608-1614.

Rösel, S., M. Allgaier, and H. P. Grossart. 2012. Long-term characterization of free-living and particle-associated bacterial communities in lake tiefwaren reveals distinct seasonal patterns. Microb Ecol 64:571-583.

Rubin, M. A., and L. G. Leff. 2007. Nutrients and other abiotic factors affecting bacterial communities in an Ohio River (USA). Microb Ecol 54:374-383.

Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. All Cold Spring Harbor Laboratory Press, New York, New York, USA.

Schiaffino, M. R., M. L. Sánchez, M. Gerea, F. Unrein, V. Balague, J. M. Gasol, and I. Izaguirre. 2016. Distribution patterns of the abundance of major bacterial and archaeal groups in Patagonian lakes. J Plankton Res 38:64-82.

Shade, A., J. G. Caporaso, J. Handelsman, R. Knight, and N. Fierer. 2013. A meta-analysis of changes in bacterial and archaeal communities with time. The ISME J 7:1493-1506.

Smith, R. L., and T. M. Smith. 2001. Ecología. 4ta edición. Pearson Educación S.A., Madrid, España.

Staley, C., T. J. Gould, P. Wang, J. Phillips, J. B. Cotner, and M. J. Sadowsky. 2015. Species sorting and seasonal dynamics primarily shape bacterial communities in the UpperMississippi River. Sci Total Environ 505:435-445.

Strickland, M. S., C. Lauber, N. Fierer, and M. A. Bradford. 2009. Testing the functional significance of microbial community composition. Ecology 90:441-451.

Tiquia, S. M. 2011. Extracellular Hydrolytic Enzyme Activities of the Heterotrophic Microbial Communities of the Rouge River: An Approach to Evaluate Ecosystem Response to Urbanization. Microb Ecol 62:679-689.

Vladár, P., A. Rusznyák, K. Márialigeti, and A. K. Borsodi. 2008. Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach. Microb Ecol 56:64-75.

Yachi, S., and M. Loreau. 1999. Biodiversity and ecosystems productivity in a fluctuating environment: the insurance hypothesis. P Natl Acad Sci Usa 96:1463-1468.

Yeates, C., M. Gillings, A. Davison, N. Altavilla, and D. Veal. 1997. PCR amplification of crude microbial DNA extracted from soil. Lett Appl Microbiol 25:303-307.

Wang, P., B. Chen, R. Yuan, C. Li, and Y. Li. 2016. Characteristics of aquatic bacterial community and the influencing factors in an urban river. Sci Total Environm 569-570:382-389.

Wei, G., M. Li, F. Li, H. Li, and Z. Gao. 2016. Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl Microbiol Biotechnol 100:9683-9697.

Wetzel, R. G. 2001. Limnology. Lake and River Ecosystems, 3rd edition. Academic Press, San Diego, USA.

Zeng, J., L. Yang, J. Li, Y. Liang, L. Xiao, L. Jiang, and D. Zhao. 2009. Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques. World J Microbiol Biotechnol 25:225-233.

Zhang, W., L. S. Song, J. S. Ki, C. K. Lau, X. D. Li, P. Y. Qian. 2008. Microbial Diversity in polluted harbor sediments II: sulfate-reducing bacterial community assessment using terminal restriction fragment length polymorphism and clone library of dsrAB gene. Estuar Coast Shelf S 76:682-691.

Cambios en la composición de la comunidad bacteriana de diferentes hábitats a lo largo de un río contaminado ( Río Suquía, Córdoba, Argentina)

Downloads

Published

2017-04-07

How to Cite

Merlo, C., Amé, M. V., Bertrand, L., & Abril, A. (2017). Changes in the bacterial community composition of different habitats along a polluted river (Suquía River, Cordoba, Argentina). Ecología Austral, 27(1), 072–084. https://doi.org/10.25260/EA.17.27.1.0.401