Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 5

gen. nov., sp. nov., an ammonia-tolerant formate-utilizing bacterium originating from a biogas process Open Access

Abstract

A strictly anaerobic bacterial strain, designated as AMB_02, was isolated from a propionate enrichment culture obtained from a high-ammonia biogas digester. The cells were anaerobic and coccoid (0.5 µm), often appearing as diplococci or in a short chain of three to four cells. Growth was observed between 20 and 45 °C (optimum at 37–39 °C), with an initial pH of 6.5–9.0 (optimum pH 8.0–8.5), and the species tolerated up to 0.8 M NHCl and 0.5 M NaCl. The major cellular fatty acids were C (31.6%), C (14.6%) and C (13.3%). AMB_02 grew with formate, carbohydrates and , including asparagine, histidine, tryptone and tryptophan. Acetate was the major product formed. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AMB_02 was most closely related to the species (92.5%). The genome of strain AMB_02 was 2.5 Mb in length with a G+C content of 34.8 mol%, and 2,354 protein-coding genes were predicted. Furthermore, genes coding for the reductive glycine pathway potentially used for formate metabolism were identified. Comparative genomic analysis of AMB_02 revealed the closest similarity to [21.2% digital DNA–DNA hybridization (dDDH) and 77.4% average identity (ANI)] and to (4.4% dDDH and 76.9% ANI). Based on the phenotypic characteristics and phylogenetic analyses, AMB_02 is regarded as a novel genus, , within the family for which the species name is proposed. The type strain is AMB_02=DSM 110248=JCM 39108.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ammonia tolerant , anaerobic digestion , formate metabolism , Microaceticoccus and Peptoniphilaceae
Funding
This study was supported by the:
  • European Research Council (Award 948138)
    • Principle Award Recipient: MariaWesterholm
  • Svenska Forskningsrådet Formas (Award 2018-01341)
    • Principle Award Recipient: GeorgeCheng
  • Svenska Forskningsrådet Formas (Award 2018-01341)
    • Principle Award Recipient: AnnaSchnürer
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006773
2025-05-08
2025-05-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/5/ijsem006773.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006773&mimeType=html&fmt=ahah

References

  1. Sevillano CA, Pesantes AA, Peña Carpio E, Martínez EJ, Gómez X. Anaerobic digestion for producing renewable energy-the evolution of this technology in a new uncertain scenario. Entropy 2021; 23:145 [View Article] [PubMed]
     [Google Scholar]
  2. Westerholm M, Schnürer A, Westerholm M, Schnürer A. n.d. Microbial responses to different operating practices for biogas production systems. IntechOpen Epub ahead of print 12 February 2019 [View Article]
     [Google Scholar]
  3. Kovács E, Wirth R, Maróti G, Bagi Z, Rákhely G et al. Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition. PLoS One 2013; 8:e77265 [View Article] [PubMed]
     [Google Scholar]
  4. Kovács E, Wirth R, Maróti G, Bagi Z, Nagy K et al. Augmented biogas production from protein-rich substrates and associated metagenomic changes. Bioresour Technol 2015; 178:254–261 [View Article] [PubMed]
     [Google Scholar]
  5. Westerholm M, Moestedt J, Schnürer A. Biogas production through syntrophic acetate oxidation and deliberate operating strategies for improved digester performance. Applied Energy 2016; 179:124–135 [View Article]
     [Google Scholar]
  6. Bonk F, Popp D, Weinrich S, Sträuber H, Kleinsteuber S et al. Ammonia inhibition of anaerobic volatile fatty acid degrading microbial communities. Front Microbiol 201826 January 2023 9:2921 [View Article] [PubMed]
     [Google Scholar]
  7. Westerholm M, Hansson M, Schnürer A. Improved biogas production from whole stillage by co-digestion with cattle manure. Bioresour Technol 2012; 114:314–319 [View Article] [PubMed]
     [Google Scholar]
  8. Johnson CN, Whitehead TR, Cotta MA, Rhoades RE, Lawson PA. Peptoniphilus stercorisuis sp. nov., isolated from a swine manure storage tank and description of Peptoniphilaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:3538–3545 [View Article] [PubMed]
     [Google Scholar]
  9. Patel NB, Tito RY, Obregón-Tito AJ, O’Neal L, Trujillo-Villaroel O et al. Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in peru. Anaerobe 2015; 32:43–48 [View Article] [PubMed]
     [Google Scholar]
  10. Bilen M, Mbogning Fonkou MD, Nguyen TT, Richez M, Daoud Z et al. Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono-genomics description. Microbiologyopen 2019; 8:e00735 [View Article] [PubMed]
     [Google Scholar]
  11. Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A. Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches. Microb Biotechnol 2018; 11:680–693 [View Article] [PubMed]
     [Google Scholar]
  12. Westerholm M, Roos S, Schnürer A. Syntrophaceticus schinkii gen. nov., sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter. FEMS Microbiol Lett 2010; 309:100–104 [View Article] [PubMed]
     [Google Scholar]
  13. Westerholm M, Calusinska M, Dolfing J. Syntrophic propionate-oxidizing bacteria in methanogenic systems. FEMS Microbiol Rev 2021fuab057 [View Article] [PubMed]
     [Google Scholar]
  14. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  20. Patel NB, Obregón-Tito AJ, Tito RY, Trujillo-Villaroel O, Marin-Reyes L et al. Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member. Int J Syst Evol Microbiol 2019; 69:1142–1148 [View Article] [PubMed]
     [Google Scholar]
  21. Murdoch DA, Shah HN. Reclassification of Peptostreptococcus magnus (Prevot 1933) Holdeman and Moore 1972 as Finegoldia magna comb. nov. and Peptostreptococcus micros (Prevot 1933) Smith 1957 as Micromonas micros comb. nov. Anaerobe 1999; 5:555–559 [View Article]
     [Google Scholar]
  22. Schnürer A, Singh A, Bi S, Qiao W, Westerholm M. Miniphocaeibacter halophilus sp. nov., an ammonium-tolerant acetate-producing bacterium isolated from a biogas system. Int J Syst Evol Microbiol 2022; 72:005328 [View Article] [PubMed]
     [Google Scholar]
  23. Tindall BJ, Euzéby JP. Proposal of Parvimonas gen. nov. and Quatrionicoccus gen. nov. as replacements for the illegitimate, prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002, respectively. Int J Syst Evol Microbiol 2006; 56:2711–2713 [View Article] [PubMed]
     [Google Scholar]
  24. Sun H, Brandt C, Schnürer A. Long-read DNA preparation for bacterial isolates; 2020 https://www.protocols.io/view/long-read-dna-preparation-for-bacterial-isolates-64ghgtw accessed 24 January 2023
  25. Wick R. Filtlong: Quality Filtering Tool for Long Reads; 2024 https://github.com/rrwick/Filtlong accessed 4 January 2024
  26. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  27. GitHub - nanoporetech/medaka Sequence correction provided by ONT Research. n.d https://github.com/nanoporetech/medaka accessed 4 January 2024
  28. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  29. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2020; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  30. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  31. Emms DM, Kelly S. STAG: species tree inference from all genes. Evol Biol 2018 [View Article]
     [Google Scholar]
  32. Emms DM, Kelly S. STRIDE: species tree root inference from gene duplication events. Mol Biol Evol 2017; 34:3267–3278 [View Article] [PubMed]
     [Google Scholar]
  33. Rambaut A. FigTreev1.4.4 2018 http://tree.bio.ed.ac.uk/software/figtree/
  34. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  35. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes; 2016 Epub ahead of print 2016 [View Article]
  36. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
     [Google Scholar]
  37. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
     [Google Scholar]
  38. Rodríguez RL, Konstantinidis K. Bypassing cultivation to identify bacterial species: culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  39. Park M-J, Kim YJ, Park M, Yu J, Namirimu T et al. Establishment of genome based criteria for classification of the family desulfovibrionaceae and proposal of two novel genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205 [View Article] [PubMed]
     [Google Scholar]
  40. Ragsdale SW, Pierce E. Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. Biochim Biophys Acta 2008; 1784:1873–1898 [View Article] [PubMed]
     [Google Scholar]
  41. Song Y, Lee JS, Shin J, Lee GM, Jin S et al. Functional cooperation of the glycine synthase-reductase and wood-ljungdahl pathways for autotrophic growth of Clostridium drakei. Proc Natl Acad Sci USA 2020; 117:7516–7523 [View Article] [PubMed]
     [Google Scholar]
  42. Li C, Hao L, Lü F, Duan H, Zhang H et al. Syntrophic acetate-oxidizing microbial consortia enriched from full-scale mesophilic food waste anaerobic digesters showing high biodiversity and functional redundancy. mSystems 2022; 7:e0033922 [View Article] [PubMed]
     [Google Scholar]
  43. Sun H, Levenfors JJ, Brandt C, Schnürer A. Characterisation of meropenem-resistant Bacillus sp. FW 1 isolated from biogas digestate. Environ Microbiol Rep 2024; 16:e13217 [View Article] [PubMed]
     [Google Scholar]
  44. Halebian S, Harris B, Finegold SM, Rolfe RD. Rapid method that aids in distinguishing gram-positive from gram-negative anaerobic bacteria. J Clin Microbiol 1981; 13:444–448 [View Article] [PubMed]
     [Google Scholar]
  45. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
     [Google Scholar]
  46. McSweeney CS, Denman SE, Mackie RI. Rumen bacteria. In Makkar HPS, McSweeney CS. eds Methods in Gut Microbial Ecology for Ruminants Dordrecht: Springer Netherlands; pp 23–37
     [Google Scholar]
  47. Westerholm M, Dolfing J, Schnürer A. Growth characteristics and thermodynamics of syntrophic acetate oxidizers. Environ Sci Technol 2019; 53:5512–5520 [View Article] [PubMed]
     [Google Scholar]
  48. Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B. Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB). Stand Genomic Sci 2016; 11:80 [View Article] [PubMed]
     [Google Scholar]
  49. Westerholm M, Roos S, Schnürer A. Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes. Syst Appl Microbiol 2011; 34:260–266 [View Article] [PubMed]
     [Google Scholar]
  50. Osuka A, Shimizu K, Ogura H, Tasaki O, Hamasaki T et al. Prognostic impact of fecal pH in critically ill patients. Crit Care 2012; 16:R119 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006773
Loading
Microaceticoccus formicicus gen. nov., sp. nov., an ammonia-tolerant formate-utilizing bacterium originating from a biogas process
Int J Syst Evol Microbiol 75, 006773 (2025); https://doi.org/10.1099/ijsem.0.006773
/content/journal/ijsem/10.1099/ijsem.0.006773
/content/journal/ijsem/10.1099/ijsem.0.006773
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error