Distinctive non-methanogen archaeal populations in anaerobic digestion

Abstract

Methanogens define the archaeal communities involved in anaerobic digestion. Recently, non-methanogen archaeal populations have been unexpectedly identified in anaerobic digestion processes. To gain insight into the ecophysiology of these uncharacterized archaeal populations, for the first time, a phylogenetic analysis was performed on a collection of non-methanogen archaeal 16S rRNA gene sequences from anaerobic digesters of broad geographic distribution, revealing a distinct clade formed by these sequences in subgroup 6 of the Miscellaneous Crenarchaeotal Group in the newly proposed archaeal phylum Bathyarchaeota. This exclusive phylogenetic assemblage enabled the development of a real-time quantitative PCR (qPCR) assay specifically targeting these non-methanogen archaeal populations in anaerobic digestion. Application of the qPCR assay in continuous anaerobic digesters indicated that these archaeal populations were minor constituents of the archaeal communities, and the abundance of these populations remained relatively constant irrespective of process perturbations. Analysis of the archaeal populations in methanogenic communities further revealed the co-occurrence of these non-methanogen archaea with acetoclastic methanogens. Nevertheless, the low abundance of non-methanogen archaea as compared with acetoclastic methanogens suggests that the non-methanogen archaeal populations were not major players in animal waste-fed methanogenic processes investigated in this study and the functions of these archaeal populations remain to be identified.

Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

“…Archaeal taxa that do not represent described methanogens classified as Euryarchaeota have previously been observed in biogas reactors, and has often been referred to as Crenarchaeota 34 , 35 . Chen and He 36 recently performed a phylogenetic analysis of previously published sequences that had been assumed to represent non-methanogenic archaea in anaerobic reactors. They found that they constituted a single phylogenetic clade related to, but distinct from, Thaumarchaeota, similar to the OTU cluster identified in our study.…”

“…They found that they constituted a single phylogenetic clade related to, but distinct from, Thaumarchaeota, similar to the OTU cluster identified in our study. Chen and He 36 referred to these as non-methanogenic archaea (NMA), and a more detailed analysis suggested that they were placed within the Group I.3 archaeal lineage, together with uncharacterized archaeal populations found in environments like flooded soils and sediments 36 . Chen and He 36 performed batch experiments and demonstrated that acetate promoted growth of NMA (compared to formate, propionate, butyrate, and methanol), but still their relative abundance of NMA was low (around 1%) compared to the aceticlastic methanogens (relative abundances of around 80%).…”

Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes

“…Notably, the Ofin site displayed evidence of a strong enrichment in methanotrophic bacteria, which would be consistent with enhanced methane formation. The Eledu site harbored the largest archaeal community, which was dominated by the crenarchaeotal MCG class that may, or may not, be involved in either production or consumption of methane ( Kubo et al, 2012 ; Evans et al, 2015 ; Chen and He, 2016 ). The Apapa sediment harbored a relatively large archaeal community that was distinguished by a dominance of acetoclastic methanogens, possibly reflecting limiting H 2 levels ( Beckmann et al, 2011 ; Beckmann and Manefield, 2014 ; Lv et al, 2015 ).…”

Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows

“…Non-methanogens have been identified in anaerobic digestion processes and gradually drew more attention in recent years. Most non-methanogen archaea in anaerobic digestion were primarily identified as Crenarchaeota [11]. While, a number of non-methanogens which participate in the ammonia-oxidizing metabolism, were classified to the phylum Thaumarchaeota [12].…”