Skip to main content
SpringerLink
Log in

Comparative analysis of the microbial community in the sediments of two constructed wetlands differentially influenced by the concentrated poultry feeding operations

  • Sediments, Sec 4 • Sediment-Ecology Interactions • Research Article
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

The aim of this study was to observe how the effluents from a massive poultry farming facility influence the microbial community in the sediment of the nearby constructed wetland, which functions as a reservoir for poultry wastes.

Materials and methods

The microbial community structures and compositions in the two neighboring constructed wetlands of Louisiana (named Big Pond and Corner Pond) were characterized and compared through a metagenomics approach using the high-throughput sequence data of a conserved 16S rDNA region (V4 region) obtained from the sediment DNA samples and the metagenomics analysis tool QIIME. Big Pond is connected to a poultry farming facility, directly influenced by the poultry wastes, while its neighboring Corner Pond is separated from the poultry house.

Results and discussion

Among the 74 phyla of prokaryotes detected from the sediments of the two wetlands, four phyla (Acidobacteria, Chloroflexi, Euryarchaeota, and Proteobacteria) were predominant in both conditions. Proteobacteria, the most predominant phylum in both wetlands, was not significantly different in its relative abundance between the two conditions. However, Alphaproteobacteria, one of the four major classes within Proteobacteria, was almost depleted in Big Pond. Within another major phylum Euryarchaeota, all the three classes known as methanogenic organisms (Methanobacteria, Methanomicrobia, and Thermoplasmata) were more abundant in Big Pond. In addition, the relative abundance of Acidobacteria was significantly reduced in Big Pond, while that of the class Dehalococcoidetes within the phylum Chloroflexi was significantly higher in Big Pond compared to Corner Pond.

Conclusions

Wastes released from an intensive poultry farming facility change significantly the relative abundance of some taxonomic groups of microorganisms in the microbial community of the wetland sediment. This study provided valuable information about the global changes of microbial community in the wetland sediments caused by the infusion of poultry wastes at various taxonomic levels.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Averhoff B, Muller V (2010) Exploring research frontiers in microbiology: recent advances in halophilic and thermophilic extremophiles. Res Microbiol 161:506–514

    Article  CAS  Google Scholar 

  • Braker G, Tiedje JM (2003) Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl Environ Microbiol 69:3476–3483

    Article  CAS  Google Scholar 

  • Braskerud BC (2001) The influence of vegetation on sedimentation and resuspension of soil particles in small constructed wetlands. J Environ Qual 30:1447–1457

    Article  CAS  Google Scholar 

  • Bridgham SD, Johnston CA, Schubauer-Berigan JP, Weishampel P (2001) Phosphorus sorption dynamics in soils and coupling with surface and pore water in riverine wetlands. Soil Sci Soc Am J 65:577–588

    Article  CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena 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 7:335–336

    Article  CAS  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624

    Article  CAS  Google Scholar 

  • Dandie CE, Burton DL, Zebarth BJ, Trevors JT, Goyer C (2007) Analysis of denitrification genes and comparison of nosZ, cnorB and 16S rDNA from culturable denitrifying bacteria in potato cropping systems. Syst Appl Microbiol 30:128–138

    Article  CAS  Google Scholar 

  • Dowd BM, Press D, Los Huertos M (2008) Agricultural nonpoint source water pollution policy: the case of California’s Central Coast. Agric Ecosyst Environ 128:151–161

    Article  Google Scholar 

  • Elsayed OF, Maillard E, Vuilleumier S, Imfeld G (2014) Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor. Sci Total Environ 499:327–335

    Article  CAS  Google Scholar 

  • Enwall K, Philippot L, Hallin S (2005) Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl Environ Microbiol 71:8335–8343

    Article  CAS  Google Scholar 

  • Findlay S, Groffman P, Dye S (2003) Effects of Phragmites australis removal on marsh nutrient cycling. Wetl Ecol Manag 11:157–165

    Article  CAS  Google Scholar 

  • Haller L, Tonolla M, Zopfi J, Peduzzi R, Wildi W, Pote J (2011) Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland). Water Res 45:1213–1228

    Article  CAS  Google Scholar 

  • He J, Sung Y, Krajmalnik-Brown R, Ritalahti KM, Loffler FE (2005) Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe. Environ Microbiol 7:1442–1450

    Article  CAS  Google Scholar 

  • Hollibaugh JT, Wong PS, Bano N, Pak SK, Prager EM, Orrego C (2001) Stratification of microbial assemblages in Mono Lake, California, and response to a mixing event. Hydrobiologia 466:45–60

    Article  CAS  Google Scholar 

  • Humayoun SB, Bano N, Hollibaugh JT (2003) Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Appl Environ Microbiol 69:1030–1042

    Article  CAS  Google Scholar 

  • Jiang C, Sun B, Li HX, Jiang YJ (2013) Determinants for seasonal change of nematode community composition under long-term application of organic manure in an acid soil in subtropical China. Eur J Soil Biol 55:91–99

    Article  Google Scholar 

  • Kang MS, Srivastava P, Tyson T, Fulton JP, Owsley WF, Yoo KH (2008) A comprehensive GIS-based poultry litter management system for nutrient management planning and litter transportation. Comput Electron Agric 64:212–224

    Article  Google Scholar 

  • Koskiaho J, Ekholm P, Raty M, Riihimaki J, Puustinen M (2003) Retaining agricultural nutrients in constructed wetlands—experiences under boreal conditions. Ecol Eng 20:89–103

    Article  Google Scholar 

  • Krzmarzick MJ, McNamara PJ, Crary BB, Novak PJ (2013) Abundance and diversity of organohalide-respiring bacteria in lake sediments across a geographical sulfur gradient. FEMS Microbiol Ecol 84:248–258

    Article  CAS  Google Scholar 

  • Lever MA (2016) A new era of methanogenesis research. Trends Microbiol 24:84–86

    Article  CAS  Google Scholar 

  • Levy-Booth DJ, Prescott CE, Grayston SJ (2014) Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biol Biochem 75:11–25

    Article  CAS  Google Scholar 

  • Ligi T, Oopkaup K, Truu M, Preem JK, Nolvak H, Mitsch WJ, Mander U, Truu J (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

    Article  Google Scholar 

  • Loffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Muller JA, Fullerton H, Zinder SH, Spormann AM (2013) Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 63:625–635

    Article  CAS  Google Scholar 

  • Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Env Microbiol 71:8228–8235

    Article  CAS  Google Scholar 

  • Marshall MM, Amos RN, Henrich VC, Rublee PA (2008) Developing SSU rDNA metagenomic profiles of aquatic microbial communities for environmental assessments. Ecol Indic 8:442–453

    Article  Google Scholar 

  • Mitsch WJ, Jorgensen SE (1989) Ecological engineering: an Introduction to ecotechnology. Wiley, New York.

  • O’Geen AT, Budd R, Gan J, Maynard JJ, Parikh SJ, Dahlgren RA (2010) Mitigating nonpoint source pollution in agriculture with constructed and restored wetlands. Adv Agron 108:1–76

    Article  Google Scholar 

  • Oren A (2014) Halophilic archaea on Earth and in space: growth and survival under extreme conditions. Philos Trans A Math Phys Eng Sci 372:2030

    Article  Google Scholar 

  • Overcash MR, Humenil FJ, Miner JR (1983) Livestock waste management. Vol 1. CRC Press, Boca Raton, FL

  • Pant HK, Reddy KR (2003) Potential internal loading of phosphorus in a wetland constructed in agricultural land. Water Res 37:965–972

    Article  CAS  Google Scholar 

  • Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC (2001) Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33:1011–1019

    Article  CAS  Google Scholar 

  • Poach ME, Hunt PG, Vanotti MB, Stone KC, Matheny TA, Johnson MH, Sadler EJ (2003) Improved nitrogen treatment by constructed wetlands receiving partially nitrified liquid swine manure. Ecol Eng 20:183–197

    Article  Google Scholar 

  • Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol 50:563–575

    Article  CAS  Google Scholar 

  • Rabotyagov SS, Kling CL, Gassman PW, Rabalais NN, Turner RE (2014) The economics of dead zones: causes, impacts, policy challenges, and a model of the Gulf of Mexico hypoxic zone. Rev Environ Econ Policy 8:58–79

    Article  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  CAS  Google Scholar 

  • Reddy KR, Kadlec RH, Flaig E, Gale PM (1999) Phosphorus retention in streams and wetlands: a review. Crit Rev Env Sci Tec 29:83–146

    Article  CAS  Google Scholar 

  • Rich JJ, Heichen RS, Bottomley PJ, Cromack K, Myrold DD (2003) Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl Environ Microbiol 69:5974–5982

    Article  CAS  Google Scholar 

  • Rysavy JP, Yan T, Novak PJ (2005) Enrichment of anaerobic polychlorinated biphenyl dechlorinators from sediment with iron as a hydrogen source. Water Res 39:569–578

    Article  CAS  Google Scholar 

  • Shutes RBE (2001) Artificial wetlands and water quality improvement. Environ Int 26:441–447

    Article  CAS  Google Scholar 

  • Sims A, Zhang YY, Galaraj S, Brown PB, Hu ZQ (2013) Toward the development of microbial indicators for wetland assessment. Water Res 47:1711–1725

    Article  CAS  Google Scholar 

  • Souza RC, Cantao ME, Vasconcelos ATR, Nogueira MA, Hungria M (2013) Soil metagenomics reveals differences under conventional and no-tillage with crop rotation or succession. Appl Soil Ecol 72:49–61

    Article  Google Scholar 

  • Sradnick A, Murugan R, Oltmanns M, Raupp J, Joergensen RG (2013) Changes in functional diversity of the soil microbial community in a heterogeneous sandy soil after long-term fertilization with cattle manure and mineral fertilizer. Appl Soil Ecol 63:23–28

    Article  Google Scholar 

  • Tanner CC, D’Eugenio J, McBride GB, Sukias JPS, Thompson K (1999) Effect of water level fluctuation on nitrogen removal from constructed wetland mesocosms. Ecol Eng 12:67–92

    Article  Google Scholar 

  • Urakawa H, Yoshida T, Nishimura M, Ohwada K (2000) Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling. Environ Microbiol 2:542–554

    Article  CAS  Google Scholar 

  • Wu HP, Zeng GM, Liang J, Zhang JC, Cai Q, Huang L, Li XD, Zhu HN, Hu CX, Shen S (2013) Changes of soil microbial biomass and bacterial community structure in Dongting Lake: impacts of 50,000 dams of Yangtze River. Ecol Eng 57:72–78

    Article  Google Scholar 

  • Zhao XQ, Yang LY, Yu ZY, Peng NY, Xiao L, Yin DQ, Qin BQ (2008) Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments. J Environ Sci China 20:224–230

    Article  Google Scholar 

Download references

Acknowledgments

This study was funded by USDA NIFA Hatch (Project no. LAB94285 for C. Y. Jeong and LAB94203 for J. H. Ham). We thank the Genomics Research Laboratory at Virginia Bioinformatics Institute (Blacksburg, VA) for the Illumina MiSeq sequencing of the sediment DNA samples.

Author information

Authors and Affiliations

  1. Red River Research Station, Louisiana State University Agricultural Center, Bossier City, LA, 71112, USA

    Chang Yoon Jeong

  2. Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA

    Jong Hyun Ham

Authors
  1. Chang Yoon Jeong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jong Hyun Ham
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jong Hyun Ham.

Additional information

Responsible editor: Haihan Zhang

Electronic supplementary material

ESM 1

(DOCX 35 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jeong, C.Y., Ham, J.H. Comparative analysis of the microbial community in the sediments of two constructed wetlands differentially influenced by the concentrated poultry feeding operations. J Soils Sediments 17, 557–566 (2017). https://doi.org/10.1007/s11368-016-1572-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11368-016-1572-5

Keywords

Search

Navigation