Applied Microbiology and Biotechnology

, Volume 103, Issue 1, pp 519–533 | Cite as

Microbial community shifts in biogas reactors upon complete or partial ammonia inhibition

  • Zuopeng LvEmail author
  • Athaydes Francisco Leite
  • Hauke Harms
  • Karin Glaser
  • Jan Liebetrau
  • Sabine Kleinsteuber
  • Marcell Nikolausz
Bioenergy and biofuels


Anaerobic digestion of nitrogen-rich substrate often causes process inhibition due to the susceptibility of the microbial community facing ammonia accumulation. However, the precise response of the microbial community has remained largely unknown. To explore the reasons, bacterial communities in ammonia-stressed reactors and control reactors were studied by amplicon pyrosequencing of 16S rRNA genes and the active methanogens were followed by terminal restriction fragment length polymorphism (T-RFLP) analyses of mcrA/mrtA gene transcripts. The results showed that the diversity of bacterial communities decreased in two parallel ammonia-inhibited reactors compared with two control reactors, but different levels of inhibitions coinciding with different community shifts were observed. In one reactor, the process was completely inhibited, which was preceded by a decreasing relative abundance of the phylum Firmicutes. Despite the same operating conditions, the process was stabilized in the parallel, partially inhibited reactor, in which the relative abundance of Firmicutes greatly increased. In particular, both ammonia-inhibited reactors lacked taxa assumed to be syntrophic bacteria (Thermoanaerobacteraceae, Syntrophomonadaceae, and Synergistaceae). Besides the predominance of the hydrogenotrophic methanogens Methanoculleus and Methanobacterium, activity of Methanosarcina and even of the strictly aceticlastic genus Methanosaeta were found to contribute at very high ammonia levels (> 9 g NH4-N L−1) in the stabilized reactor (partial inhibition). In contrast, the lack of aceticlastic activity in the parallel reactor might have led to acetate accumulation and thus process failure (complete inhibition). Collectively, ammonia was found to be a general inhibitor while accumulating acetate and thus acidification might be the key factor of complete process failure.


Methanogenesis Anaerobic digestion Syntrophic acetate oxidation Ammonia inhibition Methanosarcina 



We would like to thank Ute Lohse for technical assistance during pyrosequencing.


The work was supported by the National Natural Science Foundation of China (grant number 51708264) and Initiative and Networking Fund of the Helmholtz Association. Dr. Zuopeng Lv was supported by the China Scholarship Council (grant number 2011642040).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

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

Supplementary material

253_2018_9444_MOESM1_ESM.pdf (1.1 mb)
ESM 1 (PDF 1113 kb)


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Copyright information

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

Authors and Affiliations

  • Zuopeng Lv
    • 1
    • 2
    Email author
  • Athaydes Francisco Leite
    • 2
  • Hauke Harms
    • 2
    • 3
  • Karin Glaser
    • 2
    • 4
  • Jan Liebetrau
    • 5
  • Sabine Kleinsteuber
    • 2
  • Marcell Nikolausz
    • 2
  1. 1.The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu ProvinceJiangsu Normal UniversityXuzhouChina
  2. 2.Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research-UFZLeipzigGermany
  3. 3.German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzigGermany
  4. 4.Institute for Biological Sciences Applied Ecology and PhycologyUniversity of RostockRostockGermany
  5. 5.Department of Biochemical ConversionDeutsches Biomasseforschungszentrum gemeinnützige GmbH (DBFZ)LeipzigGermany

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