Archives of Microbiology

, Volume 199, Issue 4, pp 613–620 | Cite as

Microbial diversity in different compartments of an aquaponics system

  • Zala Schmautz
  • Andreas Graber
  • Sebastian Jaenicke
  • Alexander Goesmann
  • Ranka Junge
  • Theo H. M. Smits
Original Paper

Abstract

Aquaponics is a solution for sustainable production of fish and plants in a single semi-closed system, where nutrient-rich water from the aquaculture provides nutrients for plant growth. We examined the microbial communities within an experimental aquaponics system. Whereas the fish feces contained a separate community dominated by bacteria of the genus Cetobacterium, the samples from plant roots, biofilter, and periphyton were more similar to each other, while the communities were more diverse. Detailed examination of the data gave the first indications to functional groups of organisms in the different compartments of the aquaponic system. As other nitrifiers other than members of the genus Nitrospira were only present at low numbers, it was anticipated that Nitrospirae may perform the nitrification process in the biofilm.

Keywords

Community analysis Metagenome Tilapia Lettuce Nitrospira 

Notes

Acknowledgements

The authors thank Nadine Antenen, Alex Mathis, Beat Häcki, and Gabriele Gottschalk (ZHAW Wädenswil, CH) for their support with system maintenance and plant management during aquaponic system operation. The research was carried out with the help of initial funding of the Technology Transfer Office of the ZHAW School of Life Sciences and Facility Management. Sebastian Jaenicke and Alexander Goesmann acknowledge the support by the BMBF grant FKZ 031A533 within the de.NBI network. Funding for Theo H. M. Smits was partially provided by the SNSF in the frame of the national research program “Sustainable use of Soil as a Resource” (NRP 68, Project 406840-143144).

Compliance with ethical standards

Conflict of interest

Author Andreas Graber declares that, at the time of the experiments, he was part-time Director R&D at the ZHAW spin-off company UrbanFarmers, but that the research published in this manuscript was performed as part of his research portfolio at ZHAW. The other authors declare to have no conflict of interest.

Supplementary material

203_2016_1334_MOESM1_ESM.pdf (210 kb)
Supplementary material 1 (PDF 209 KB)

References

  1. Bittsánszky A, Gyulai G, Junge R, Schmautz Z, Komives T (2015) Plant protection in ecocycle-based agricultural systems: aquaponics as an example. In: International Plant Protection Congress (IPPC) 2015, Berlin, Germany, doi:10.13140/RG.2.1.4458.0321
  2. Brown MN, Briones A, Diana J, Raskin L (2013) Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system. FEMS Microbiol Ecol 83:17–25CrossRefPubMedGoogle Scholar
  3. Bruhn JB, Dalsgaard I, Nielsen KF, Buchholtz C, Larsen JL, Gram L (2005) Quorum sensing signal molecules (acylated homoserine lactones) in Gram-negative fish pathogenic bacteria. Dis Aquat Org 65:43–52CrossRefPubMedGoogle Scholar
  4. Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528:504–509PubMedPubMedCentralGoogle Scholar
  5. Endut A, Jusoh A, Ali N, Wan Nik WB (2011) Nutrient removal from aquaculture wastewater by vegetable production in aquaponics recirculation system. Desalin Water Treatm 32:422–430CrossRefGoogle Scholar
  6. Etyemez M, Balcázar JL (2015) Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16 S rRNA genes. Res Vet Sci 100:8–11CrossRefPubMedGoogle Scholar
  7. Fernandez D (2013) HydroBuddy: An open source nutrient calculator for hydroponics and General agriculture, v1.50. http://scienceinhydroponics.com
  8. Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, Raaijmakers JM, Duffy B, Höfte M, Blom J, Smits THM, Keel C, Maurhofer M (2016) Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME J 10:2527–2542CrossRefPubMedGoogle Scholar
  9. Garrity GM, Bell JA, Lilburn T (2005) Order III. Methylophilales ord. nov. In: Brenner DJ, Krieg NR, Staley J, Garrity GM (eds) Bergey’s Manual of Systematic Bacteriology—second edition. Volume two: the proteobacteria. Part C: The Alpha-, Beta-, Delta-, and epsilonproteobacteria. Springer, New York, pp 770–773Google Scholar
  10. Goddek S, Espinal CA, Delaide B, Jijakli MH, Schmautz Z, Wuertz S, Keesman KJ (2016) Navigating towards decoupled aquaponic systems: a system dynamics design approach. Water 8:303CrossRefGoogle Scholar
  11. Graber A, Antenen N, Junge R (2014) The multifunctional aquaponic system at ZHAW used as research and training lab. In: Maček Jerala M, Maček MA (eds) Conference VIVUS: Transmission of Innovations, Knowledge and Practical Experience into Everyday Practice, Strahinj, SloveniaGoogle Scholar
  12. Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonds. Nat Rev Microbiol 3:307–319CrossRefPubMedGoogle Scholar
  13. Hill TCJ, Walsh KA, Harris JA, Moffett BF (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43:1–11CrossRefPubMedGoogle Scholar
  14. Hu Z, Lee JW, Chandran K, Kim S, Brotto AC, Khanal SK (2015) Effect of plant species on nitrogen recovery in aquaponics. Bioresour Technol 188:92–98CrossRefPubMedGoogle Scholar
  15. Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55:485–529CrossRefPubMedGoogle Scholar
  16. Li T, Long M, Gatesoupe F-J, Zhang Q, Li A, Gong X (2015) Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing. Microb Ecol 69:25–36CrossRefPubMedGoogle Scholar
  17. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556CrossRefPubMedGoogle Scholar
  18. Munguia-Fragozo P, Alatorre-Jacome O, Rico-Garcia E, Torres-Pacheco I, Cruz-Hernandez A, Ocampo-Velazquez RV, Garcia-Trejo JF, Guevara-Gonzalez RG (2015) Perspective for aquaponics systems: “omic” technologies for microbial community analysis. Biomed Res Int 2015:480386CrossRefPubMedPubMedCentralGoogle Scholar
  19. Oshiki M, Satoh H, Okabe S (2016) Ecology and physiology of anaerobic ammonium oxidizing bacteria. Environ Microbiol 18:2784–2796CrossRefPubMedGoogle Scholar
  20. Pang M, Jiang J, Xie X, Wu Y, Dong Y, Kwok AHY, Zhang W, Yao H, Lu C, Leung FC, Liu Y (2015) Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics. Sci Rep 5:09833CrossRefGoogle Scholar
  21. Rakocy J (2007) Ten guidelines for aquaponic systems. Aquaponics J 46:14–17Google Scholar
  22. Revsberg NP, Risgaard-Petersen N, Schramm A, Nielsen LP (2006) Nitrogen transformations in stratified aquatic microbial ecosystems. Ant Leeuwenhoek 90:361–375CrossRefGoogle Scholar
  23. Rurangwa E, Verdegem MCJ (2015) Microorganisms in recirculating aquaculture systems and their management. Rev Aquacult 7:117–130CrossRefGoogle Scholar
  24. Schmautz Z (2015) Mass balance and nutrient cycling in aquaponics. Master thesis, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia, p 86Google Scholar
  25. Schrader KK, Summerfelt ST (2010) Distribution of off-flavor compounds and isolation of geosmin-producing bacteria in a series of water recirculating systems for rainbow trout culture. N Am J Aquacult 72:1–9CrossRefGoogle Scholar
  26. Sirakov I, Lutz M, Graber A, Mathis A, Staykov Y, Smits THM, Junge R (2016) Potential for combined biocontrol activity against fungal fish and plant pathogens by bacterial isolates from a model aquaponic system. Water 8:518CrossRefGoogle Scholar
  27. Somerville C, Cohen M, Pantanella E, Stankus A, Lovatelli A (2014) Small-scale aquaponic food production: integrated fish and plant farming. In: FAO Fisheries and Aquaculture Technical Paper Food and Agriculture Organization of the United Nations, Rome, Italy, p 262Google Scholar
  28. Tian H-L, Zhao J-Y, Zhang H-Y, Chi C-Q, Li B-A, Wu X-L (2015) Bacterial community shift along with the changes in operational conditions in a membrane-aerated biofilm reactor. Appl Microbiol Biotechnol 99:3279–3290CrossRefPubMedGoogle Scholar
  29. Tokuyama T, Mine A, Kamiyama K, Yabe R, Satoh K, Matsumoto H, Takahashi R, Itonaga K (2004) Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant. J Biosci Bioeng 98:309–312CrossRefPubMedGoogle Scholar
  30. Tsuchiya C, Sakata T, Sugita H (2008) Novel ecological niche of Cetobacterium somerae, an anaerobic bacterium in the intestinal tracts of freshwater fish. Lett Appl Microbiol 46:43–48PubMedGoogle Scholar
  31. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267CrossRefPubMedPubMedCentralGoogle Scholar
  32. Zou Y, Hu Z, Zhang J, Xie H, Guimbaud C, Fang Y (2016a) Effects of pH on nitrogen transformations in media-based aquaponics. Bioresour Technol 210:81–87Google Scholar
  33. Zou Y, Hu Z, Zhang J, Xie H, Liang S, Wang J, Yan R (2016b) Attempts to improve nitrogen utilization efficiency of aquaponics through nitrifies addition and filler gradation. Environ Sci Pollut Res Int 23:6671–6679Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  1. 1.Ecological Engineering Research Group, Institute for Natural Resource SciencesZurich University of Applied Sciences (ZHAW)WädenswilSwitzerland
  2. 2.UrbanFarmers AGZurichSwitzerland
  3. 3.Bioinformatics and Systems BiologyJustus-Liebig-University GiessenGiessenGermany
  4. 4.Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource SciencesZurich University of Applied Sciences (ZHAW)WädenswilSwitzerland

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