Applied Microbiology and Biotechnology

, Volume 102, Issue 12, pp 5335–5342 | Cite as

Bacterial population dynamics in recycled mushroom compost leachate

  • Katarzyna Safianowicz
  • Tina L. Bell
  • Michael A. Kertesz
Environmental biotechnology


Mushrooms are an important food crop throughout the world. The most important edible mushroom is the button mushroom (Agaricus bisporus), which comprises about 30% of the global mushroom market. This species is cultivated commercially on a selective compost that is produced predominantly from wheat straw/stable bedding and chicken manure, at a moisture content of around 70% (w/w) and temperatures of up to 80 °C. Large volumes of water are required to achieve this moisture content, and many producers therefore collect leachate from the composting windrows and bunkers (known in the industry as “goody water”) and reuse it to wet the raw ingredients. This has the benefit of recycling and saving water and has the potential to enrich beneficial microorganisms that stimulate composting, but also the risk of enhancing pathogen populations that could reduce productivity. Here, we show by 16S rRNA gene sequencing that mushroom compost leachate contains a high diversity of unknown microbes, with most of the species found affiliated with the phyla Firmicutes and Proteobacteria. However, by far the most abundant species was the thermophile Thermus thermophilus, which made up approximately 50% of the bacterial population present. Although the leachate was routinely collected and stored in an aerated central storage tank, many of the bacterial species found in leachate were facultative anaerobes. However, there was no evidence for sulfide production, and no sulfate-reducing bacterial species were detected. Because T. thermophilus is important in the high temperature phase of composting, the use of recycled leachate as an inoculum for the raw materials is likely to be beneficial for the composting process.


Recycled mushroom compost leachate Goody water Thermus thermophilus Mushroom compost Bacterial diversity 



We thank our industry partners, especially ELF Farm Supplies in Mulgrave, NSW, Australia, for their kind assistance with sampling and processing, and for their helpful advice on many aspects of mushroom composting.


This work was supported by grant MU10021 from Horticulture Innovation Australia.

Compliance with ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

253_2018_9007_MOESM1_ESM.xlsx (84 kb)
Supplemental Table S1 (XLSX 83 kb)


  1. Arrigo N, Holderegger R, Alvarez N (2012) Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library. Meth Molec Biol 888:155–175. CrossRefGoogle Scholar
  2. Beffa T, Blanc M, Lyon PF, Vogt G, Marchiani M, Fischer JL, Aragno M (1996) Isolation of Thermus strains from hot composts (60 to 80 °C). Appl Environ Microbiol 62:1723–1727PubMedPubMedCentralGoogle Scholar
  3. Bergquist PL, Gibbs MD, Morris DD, Te'o VS, Saul DJ, Moran HW (1999) Molecular diversity of thermophilic cellulolytic and hemicellulolytic bacteria. FEMS Microbiol Ecol 28:99–110. CrossRefGoogle Scholar
  4. Blanc M, Marilley L, Beffa T, Aragno M (1999) Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods. FEMS Microbiol Ecol 28:141–149. CrossRefGoogle Scholar
  5. Bolan NS, Szogi AA, Chuasavathi T, Seshadri B, Rothrock MJ, Panneerselvam P (2010) Uses and management of poultry litter. Worlds Poult Sci J 66:673–698. CrossRefGoogle Scholar
  6. 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. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chang S-T, Miles PG (2004) Mushrooms: cultivation, nutritional value, medicinal effect and environmental impact, 2nd edn. CRC Press, Boca RatonCrossRefGoogle Scholar
  8. Charif D, Lobry JR (2007) Seqin{R} 1.0-2: a contributed package to the {R} project for statistical computing devoted to biological sequences retrieval and analysis. In: Bastolla U, Porto M, Roman HE, Vendruscolo M (eds) Structural approaches to sequence evolution: Molecules, networks, populations. Springer, New York, pp 207–232CrossRefGoogle Scholar
  9. Collado L, Figueras MJ (2011) Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clin Microbiol Rev 24:174–192. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Constantine W, Hesterberg T, Wittkowski K, Song T, Kaluzny S (2016) Supplemental S-PLUS functionality in R. R package version 1.2–2. R Foundation for Statistical Computing, Vienna, Austria. Accessed 1 Nov 2017
  11. Guo MX (2005) Groundwater quality under the influence of spent mushroom substrate weathering. J Environ Monit 7:1007–1012. CrossRefPubMedGoogle Scholar
  12. Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, Merkl R, Gottschalk G, Fritz HJ (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22:547–553. CrossRefPubMedGoogle Scholar
  13. Jurak E, Punt AM, Arts W, Kabel MA, Gruppen H (2015) Fate of carbohydrates and lignin during composting and mycelium growth of Agaricus bisporus on wheat straw based compost. PLoS One 10:e0138909. CrossRefPubMedPubMedCentralGoogle Scholar
  14. Kaplan LA, Standley LJ, Newbold JD (1995) Impact on water quality of high and low density applications of spent mushroom substrate to agricultural lands. Compost Sci Util 3:55–63. CrossRefGoogle Scholar
  15. Kertesz M, Safianowicz K, Bell T (2016) New insights into the microbial communities and biological activities that define mushroom compost. Sci Cult Edible Fungi 19:161–165Google Scholar
  16. Kertesz MA, Thai M (2018) Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms. Appl Microbiol Biotechnol 102:1639–1650. CrossRefPubMedGoogle Scholar
  17. Li X (2005) PROcess: Ciphergen SELDI-TOF processing. R package version 1.54.0. R Foundation for Statistical Computing, Vienna, Austria. Accessed 1 Nov 2017
  18. Lyon PF, Beffa T, Blanc M, Auling G, Aragno M (2000) Isolation and characterization of highly thermophilic xylanolytic Thermus thermophilus strains from hot composts. Can J Microbiol 46:1029–1035. CrossRefPubMedGoogle Scholar
  19. Lyons G, Kilpatrick M, Sharma HSS, Noble R, Dobrovin-Pennington A, Hobbs P, Andrews F, Carmichael E (2008) Characterization of recycled mushroom compost leachate by chemical analysis and thermogravimetry-mass spectrometry. J Agric Food Chem 56:6488–6497. CrossRefPubMedGoogle Scholar
  20. McGee CF, Byrne H, Irvine A, Wilson J (2017) Diversity and dynamics of the DNA and cDNA-derived bacterial compost communities throughout the Agaricus bisporus mushroom cropping process. Ann Microbiol 67:751–761. CrossRefGoogle Scholar
  21. Noble R (2006) Improving the efficiency and environmental impact of mushroom composting. Final Report, M 3e HortLINK Project CSA6365/HL0163LMU. Warwick HRI, WarwickGoogle Scholar
  22. Noble R, Dobrovin-Pennington A, Wright C, Hobbs PJ, Williams J (2009) Aerating recycled water on mushroom composting sites affects its chemical analysis and the characteristics of odor emissions. J Environ Qual 38:1493–1500. CrossRefPubMedGoogle Scholar
  23. Noble R, Hobbs PJ, Dobrovin-Pennington A, Misselbrook TH, Mead A (2001) Olfactory response to mushroom composting emissions as a function of chemical concentration. J Environ Qual 30:760–767CrossRefPubMedGoogle Scholar
  24. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Henry M, Stevens H, Wagner H (2016) vegan: Community ecology package in R. R package version 2.3-4. R Foundation for Statistical Computing, Vienna, Austria. Accessed 1 Nov 2017
  25. Perttula M, Ratto M, Kondradsdottir M, Kristjansson JK, Viikari L (1993) Xylanases of thermophilic bacteria from Icelandic hot springs. Appl Microbiol Biotechnol 38:592–595CrossRefGoogle Scholar
  26. R Core team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Accessed 1 Nov 2017
  27. Racine JS (2012) RStudio: a platform-independent IDE for R and Sweave. J Appl Econ 27:167–172. CrossRefGoogle Scholar
  28. Regueiro L, Carballa M, Lema JM (2014) Outlining microbial community dynamics during temperature drop and subsequent recovery period in anaerobic co-digestion systems. J Biotechnol 192:179–186. CrossRefPubMedGoogle Scholar
  29. Rothrock MJ, Cook KL, Warren JG, Eiteman MA, Sistani K (2010) Microbial mineralization of organic nitrogen forms in poultry litters. J Environ Qual 39:1848–1857. CrossRefPubMedGoogle Scholar
  30. Royse DJ (2014) A global perspective on the high five: Agaricus, Pleurotus, Lentinula, Auricularia and Flammulina. In: Singh M (ed) Proceedings of the 8th International Conference on Mushroom Biology and Mushroom Products. New Delhi, pp 1–6Google Scholar
  31. Ryckeboer J, Mergaert J, Vaes K, Klammer S, De Clercq D, Coosemans J, Insam H, Swings J (2003) A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol 53:349–410Google Scholar
  32. Szekely A, Sipos R, Berta B, Vajna B, Hajdu C, Marialigeti K (2009) DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microb Ecol 57:522–533. CrossRefPubMedGoogle Scholar
  33. Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer, New YorkCrossRefGoogle Scholar
  34. Winsley T, van Dorst JM, Brown MV, Ferrari BC (2012) Capturing greater 16S rRNA gene sequence diversity within the domain Bacteria. Appl Environ Microbiol 78:5938–5941. CrossRefPubMedPubMedCentralGoogle Scholar
  35. Wu YW, Joshua C, Eichorst SA, Gladden JM, Simmons BA, Singer SW (2015) Genomic analysis of xylose metabolism in members of the Deinoccocus-Thermus phylum from thermophilic biomass-deconstructing bacterial consortia. BioEnergy Res 8:1031–1038. CrossRefGoogle Scholar
  36. Xie Y (2013) knitr: a general purpose package for dynamic report generation in R. R Package version 1.20. R Foundation for Statistical Computing, Vienna, Austria. Accessed 1 Nov 2017

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Katarzyna Safianowicz
    • 1
  • Tina L. Bell
    • 1
  • Michael A. Kertesz
    • 1
  1. 1.Sydney Institute of Agriculture, School of Life and Environmental SciencesThe University of SydneySydneyAustralia

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