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Ecological diversity of sediment rhizobacteria associated with Phragmites australis along a drainage canal in the Yellow River watershed

  • Sediments, Sec 4 • Sediment-Ecology Interactions • Research Article
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Abstract

Purpose

Spatial distribution on a regional scale of the rhizobacterial communities of Phragmites australis stands was investigated along the Yellow River watershed, China.

Materials and methods

Samples were collected along a secondary and the main drainage canals. Amplified ribosomal intergenic spacer analysis (ARISA) and pyrosequencing were performed to study the diversity of microbial communities. Bacterial functionality was characterized using a functional inference-based (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt) approach.

Results and discussion

Microbial community structure resulted to be primarily driven by phosphorus, nitrogen, mercury, chromium, and nickel. At genus level, taxa related to bioremediation, in particular Thiobacillus and Flavobacterium, and plant growth-promoting bacteria, such as Lysobacter, were found to be stably associated with P. australis. Genera related to fecal contamination such as Faecalibacterium, were recorded in three sampling sites. Rhizobacterial communities showed a significant fraction of taxa related to the xenobiotic metabolism and degradation.

Conclusions

Rhizobacterial communities were influenced by the multiple effects of the different environmental parameters. Moreover, the rhizosphere of P. australis can be considered potentially a source of bacterial taxa useful for bioremediation and growth-promoting activities of plants.

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References

  • Barton DN (2005) Report: economic analysis of the value of water in alternative uses in the Lake Wuliangsuhai catchment, Norwegian Institute of Water Research

  • BCPG (2010) Wuliangsuhai comprehensive treatment plan (Wuliangsuhai Zonghe Zhili Guihua). Bayannur City People’s Government, Bayannur

    Google Scholar 

  • Besemer K (2015) Biodiversity, community structure and function of biofilms in stream ecosystems. Res Microbiol 166:774–781

    Article  Google Scholar 

  • Brusetti L, Borruso L (2014) Diversity and role of rhizobacteria associated to reed stands (Phragmites australis). In: Cirella GT, Zerbe S (eds) Sustainable water management and wetland restoration strategies in northern China. Bu Press, Bozen-Bolzano, pp. 83–93

    Google Scholar 

  • Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70:6147–6156

    Article  CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:33–56

    Article  Google Scholar 

  • Chaudhry Q, Schröder P, Werck-Reichhart D, Grajek W, Marecik R (2002) Prospects and limitations of phytoremediation for the removal of persistent pesticides in the environment. Environ Sci Pollut Res 9:4–17

    Article  CAS  Google Scholar 

  • Clevering OA, Lissner J (1999) Taxonomy, chromosome numbers, clonal diversity and population dynamics of Phragmites australis. Aquat Bot 64:185–208

    Article  Google Scholar 

  • Cruz AF, Hamel C, Hanson K, Selles F, Zentner RP (2009) Thirty-seven years of soil nitrogen and phosphorus fertility management shapes the structure and function of the soil microbial community in a Brown Chernozem. Plant Soil 315:173–184

    Article  CAS  Google Scholar 

  • Coban O, Kuschk P, Kappelmeyer U, Spott O, Martienssen M, Jetten MS, Knoeller K (2015) Nitrogen transforming community in a horizontal subsurface-flow constructed wetland. Water Res 74:203–212

    Article  CAS  Google Scholar 

  • Dash S, Jin C, Lee OO, Xu Y, Qian PY (2009) Antibacterial and antilarval-settlement potential and metabolite profiles of novel sponge-associated marine bacteria. J Ind Microbiol Biotechnol 36:1047–1056

    Article  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461

    Article  CAS  Google Scholar 

  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200

    Article  CAS  Google Scholar 

  • Ellis RJ, Neish B, Trett MW, Best JG, Weightman AJ, Morgan P, Fry JC (2001) Comparison of microbial and meiofaunal community analyses for determining impact of heavy metal contamination. J Microbiol Methods 45:171–185

    Article  CAS  Google Scholar 

  • Fernandes JP, Almeida CM, Pereira AC, Ribeiro IL, Reis I, Carvalho P, Basto MC, Mucha AP (2015) Microbial community dynamics associated with veterinary antibiotics removal in constructed wetlands microcosms. Bioresour Technol 182:26–33

    Article  CAS  Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. PNAS 103:626–631

    Article  CAS  Google Scholar 

  • Glick BR (2010) Using soil bacteria to facilitate phytoremediation. Biotechnol Adv 28:367–374

    Article  CAS  Google Scholar 

  • Gomez C, Bosecker K (1999) Leaching heavy metals from contaminated soil by using Thiobacillus ferrooxidans or Thiobacillus thiooxidans. Geomicrobiol J 16:233–244

    Article  CAS  Google Scholar 

  • Güsewell S, Klötzli F (2000) Assessment of aquatic and terrestrial reed (Phragmites australis) stands. Wetl Ecol Manag 8:367–373

    Article  Google Scholar 

  • Hazrat A, Ezzat K, Muhammad AS (2013) Phytoremediation of heavy metals—concepts and applications. Chemosphere 91:869–881

    Article  Google Scholar 

  • Hernández M, Dumont MG, Yuan Q, Conrad R (2015) Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Appl Environ Microbiol 81:2244–2253

    Article  Google Scholar 

  • Jog R, Pandya M, Nareshkumar G, Rajkumar S (2014) Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth. Microbiology 160:778–788

    Article  CAS  Google Scholar 

  • Kleindienst S, Herbst FA, Stagars M, Frederick N, Bergen M, Seifert J, Peplies J, Amann R, Musat F, Lueders T, Knittel K (2014) Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. Isme J 8:2029–2044

    Article  CAS  Google Scholar 

  • Köbbing JF, Thevs N, Zerbe S (2013) The utilisation of reed (Phragmites australis): a review. Mires Peat 13:1–14

    Google Scholar 

  • Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821

    Article  CAS  Google Scholar 

  • Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community composition at the continental scale. Appl Environ Microbiol 75:5111–5120

    Article  CAS  Google Scholar 

  • Lawrence JR, Chenier MR, Roy R, Beaumier D, Fortin N, Swerhone GDW, Neu TR, Greer CW (2004) Microscale and molecular assessment of impacts of nickel, nutrients, and oxygen level on structure and function of river biofilm communities microscale and molecular assessment of impacts of nickel, nutrients, and oxygen level on structure and function of river biofilm communities. Appl Environ Microbiol 70:4326–4339

    Article  CAS  Google Scholar 

  • Lear G, Lewis GD (2009) Impact of catchment land use on bacterial communities within stream biofilms. Ecol Indic 9:848–855

    Article  CAS  Google Scholar 

  • Li YH, Zhu JN, Zhai ZH, Zhang Q (2010) Endophytic bacterial diversity in roots of Phragmites australis in constructed Beijing Cuihu wetland (China). FEMS Microbiol Lett 309:84–93

    CAS  Google Scholar 

  • Ma Y, Prasad MNV, Rajkumar M, Freitas H (2011) Plant growth promoting rhizobacteria and endophytes accelerate phytoremediation of metalliferous soils. Biotechnol Adv 29:248–258

    Article  CAS  Google Scholar 

  • Micsinai A, Borsodi AK, Csengeri V, Horváth A, Oravecz O, Nikolausz M, Reskóné MN, Márialigeti K (2003) Rhizome-associated bacterial communities of healthy and declining reed stands in Lake Velencei, Hungary. Hydrobiologia 509:707–713

    Article  Google Scholar 

  • Mothes F, Reiche N, Fiedler P, Moeder M, Borsdorf H (2010) Capability of headspace based sample preparation methods for the determination of methyl tert-butyl ether and benzene in reed (Phragmites australis) from constructed wetlands. Chemosphere 80:396–403

    Article  CAS  Google Scholar 

  • Muhammad AQ, Khan QM, Sessitsch A (2014) Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants. Chemosphere 117:232–242

    Article  Google Scholar 

  • Park JH, Kim R, Aslam Z, Jeon CO, Chung YR (2008) Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. Int J Syst Evol Microbiol 58:387–392

    Article  CAS  Google Scholar 

  • Pernthaler J (2013) Freshwater microbial communities. In: Rosenberg E, DeLong E, Edward F, Lory S, Stephen L, Stackebrandt E, DeLong E, Fabiano T (eds) The prokaryotes. Springer, Berlin, pp. 97–112

    Chapter  Google Scholar 

  • R Core Team (2012) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. URL:http://www.R-project.org/

  • Rajilić-Stojanović M, de Vos WM (2014) The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 38:996–1047

    Article  Google Scholar 

  • Ratnaweera H, Fejes J, Yawei L, Lindblim E, Faafeng B, Ruden F (2008) Report: Lake Wuliangsuhai comprehensive study extension management and control plan inner Mongolia Lake restoration project

  • Sun MY, Dafforn K, Brown MV, Johnston EL (2012) Bacterial communities are sensitive indicators of contaminant stress. Mar Pollut Bull 64:1029–1038

    Article  CAS  Google Scholar 

  • Sun Y, Wang T, Peng X, Wang P, Lu Y (2016) Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing. Environ Sci Pollut Res Int. doi:10.1007/s11356-016-6055-0

    Google Scholar 

  • Thevs N, Ott K, Kerschbaumer L, He P (2014) Study areas: the Heihe River basin and Wuliangsuhai Lake at the Hetao Irrigation District. In: Cirella GT, Zerbe S (eds) Sustainable water management and wetland restoration strategies in northern China. Bu Press, Bozen-Bolzano, pp. 27–37

    Google Scholar 

  • Vladár P, Rusznyák A, Márialigeti K, Borsodi AK (2007) 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

    Article  Google Scholar 

  • Vymazal J, Kröpfelová L, Švehla J, Chrastný V, Štíchová J (2009) Trace elements in Phragmites australis growing in constructed wetlands for treatment of municipal wastewater. Ecol Eng 35:303–309

    Article  Google Scholar 

  • Wang GL, Wang L, Chen HH, Shen B, Li SP, Jiang JD (2011) Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil. Int J Syst Evol Microbiol 61:674–679

    Article  CAS  Google Scholar 

  • Wang T, Wang P, Meng J, Liu S, Lu Y, Khim JS, Giesy JP (2016) A review of sources, multimedia distribution and health risks of perfluoroalkyl acids (PFAAs) in China. Chemosphere 129:87–99

    Article  Google Scholar 

  • Whiteley AS, Bailey MJ (2000) Bacterial community structure and physiological state within an industrial phenol bioremediation system. Appl Environ Microbiol 66:2400–2407

    Article  CAS  Google Scholar 

  • Yamian Z, Yifei J, Shengwu J, Qing Z, Duoduo F, Yumin G, Guangchun L (2012) Wuliangsuhai wetlands: a critical habitat for migratory water birds. JoRE 3:316–323

    Google Scholar 

  • Yergeau E, Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, Greera CW (2012) Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl Environ Microbiol 78:7626–7637

    Article  CAS  Google Scholar 

  • Zhang W, Wu X, Liu G, Chen T, Zhang G, Dong Z, Yang X, Hu P (2013) Pyrosequencing reveals bacterial diversity in the rhizosphere of three Phragmites australis. Ecotypes Geomicrobiol J 30:593–599

    Article  CAS  Google Scholar 

  • Zheng G, Yampara-Iquise H, Jones JE, Carson CA (2009) Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces. J Appl Microbiol 106:634–641

    Article  CAS  Google Scholar 

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Acknowledgments

This work was funded by the Kurt–Eberhard–Bode Foundation within the Stifterverband für die Deutsche Wissenschaft (SuWaRest Project) (CUP n. I41J10000880007), and by the Foundation of the Free University of Bozen/Bolzano. Manuscript style has been edited end revised by Peter Brannick.

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Authors and Affiliations

  1. Faculty of Science and Technology, Free University of Bozen/Bolzano, piazza Università 5, 39100, Bolzano, Italy

    Luigimaria Borruso, Alfonso Esposito, Alessia Bani, Sonia Ciccazzo, Marianna Papa, Stefan Zerbe & Lorenzo Brusetti

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  1. Luigimaria Borruso
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  2. Alfonso Esposito
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  3. Alessia Bani
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  4. Sonia Ciccazzo
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  6. Stefan Zerbe
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  7. Lorenzo Brusetti
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Correspondence to Lorenzo Brusetti.

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Responsible editor: Haihan Zhang

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Borruso, L., Esposito, A., Bani, A. et al. Ecological diversity of sediment rhizobacteria associated with Phragmites australis along a drainage canal in the Yellow River watershed. J Soils Sediments 17, 253–265 (2017). https://doi.org/10.1007/s11368-016-1498-y

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  • DOI: https://doi.org/10.1007/s11368-016-1498-y

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