Abstract
The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.
Similar content being viewed by others
References
Aeberhard S, Coomans D, Devel O (1993) Improvements to the classification performance of Rda. J Chemometr 7(2):99–115
Aguirre-von-Wobeser E, Eguiarte LE, Souza V, Soberon-Chavez G (2015) Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments. Front Microbiol 6:490
Braun BS, Freiden R, Lessnick SL, May WA, Denny C (1995) Identification of target genes for the Ewing’s Sarcoma EWS/FLI fusion protein by representational difference analysis (RDA). Mol Cell Biol 15(8):4623–4630
Buttigieg PL, Ramette A (2014) A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses. FEMS Microbiol Ecol 90(3):543–550
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ et al (2011) Global patterns of 16S rDNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 108:4516–4522
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N et al (2012) Ultra-high-throughput microbial community analysis on the IlluminaHiSeq and MiSeqplatforms. ISME J 6:1621–1624
Crump BC, Peterson BJ, Raymond PA et al (2009) Circumpolar synchrony in big river bacterioplankton. Proc Natl Acad Sci USA 106(50):21208–21212
Dang HY, Zhang XX, Sun J, Li TG, Zhang ZN, Yang GP (2008) Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. Microbiology 154:2084–2095
Daniels L, Budding AE, de Korte N et al (2014) Fecal microbiome analysis as a diagnostic test for diverticulitis. Eur J Clin Microbiol 33(11):1927–1936
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200
Edwards JE, McEwan NR, Travis AJ, Wallace RJ (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie Van Leeuwenhoek 86(3):263–281
Euzeby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47(2):590–592
Fogg GE (1996) Algae: An introduction to phycology. In: van den Hoek C, Mann DC, Jahns HJ (eds). Nature 381(6584):660–660
Garneau C, Sauvage S, Probst A, Sánchez-Pérez JM (2015) Modelling of trace metal transfer in a large river under different hydrological conditions (the Garonne River in southwest France). Ecol Model 306:195–204
Gedalanga P, Kotay SM, Sales CM, Butler CS, Goel R, Mahendra S (2013) Novel applications of molecular biological and microscopic tools in environmental engineering. Water Environ Res 85(10):917–950
Kerstens HHD, Crooijmans RPMA, Veenendaal A et al (2009) Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genom 10:479
Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437(7058):543–546
Leps J, Šmilauer P (2003) Multivariate analysis of ecological data using CANOCO. Cambridge University Press, New York
Ligi T, Oopkaup K, Truu M et al (2014) Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing. Ecol Eng 72:56–66
Mudarris M, Austin B, Segers P, Vancanneyt M, Hoste B, Bernardet JF (1994) Flavobacterium scophthalmum sp. nov., a pathogen of turbot (Scophthalmus maximus L.). Int J Syst Bacteriol 44(3):447–453
Newete SW, Erasmus BFN, Weiersbye IM, Byrne MJ (2014) The effect of water pollution on biological control of water hyacinth. Biol Control 79:101–109
Salmond GPC, Whittenbury R (1985) Biology of microorganisms, 4th edition—Brock TD, Smith DW, Madigan MT. Nature 314(6006):49–49
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM et al (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci 103:12115–12120
Solie LP (1980) The development of high-performance Rda devices. IEEE Sonic Ultrason Trans 27(3):164–165
Staley C, Unno T, Gould TJ et al (2013) Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. J Appl Microbiol 115(5):1147–1158
Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ (2014) Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River. Front Microbiol 5:524
Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ (2015) Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River. Sci Total Environ 505:435–445
State Environmental Protection Administration (2002) Determination methods for examination of water and wastewater. China Environmental Science Press, Beijing
Ter Braak CJF (1988) CANOCO—an extension of DECORANA to analyze species-environment relationships. Vegetatio 75(3):159–160
Wang L, Xu PH, Song T, Li HE (2011) Variation tendency of water quality and its causing effect of the Fenghe River. J Northwest Univ (Nat Sci Ed) 3:29
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rDNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
Ward DM, Weller R, Bateson MM (1990) 16s rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345(6270):63–65
Xing Y, Si YX, Hong C, Li Y (2015) Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil. Arch Environ Contam Toxicol 69(1):20–31
Xu JX (1990) Complex response in adjustment of the Weihe River channel to the construction of the Sanmenxia reservoir. Z Geomorphol 34(2):233–245
You J, Das A, Dolan EM, Hu Z (2009) Ammonia-oxidizing archaea involved in nitrogen removal. Water Res 43(7):1801–1809
Acknowledgments
This study was supported by the National Natural Science Foundation of China (Grants Nos. 51178048 and 51378064) and BNU Discretionary Foundation (Grant No. 2014KJJCB22).
Author information
Authors and Affiliations
Corresponding author
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Lu, S., Sun, Y., Zhao, X. et al. Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China. Arch Environ Contam Toxicol 71, 122–132 (2016). https://doi.org/10.1007/s00244-016-0277-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00244-016-0277-5