Archaeal diversity during composting of pig manure and mushroom cultural waste based on 16S rRNA sequence

Abstract

Archaeal diversity during the composting process of pig manure and mushroom culture waste using a field-scale composter was investigated by a culture-independent approach. Metagenomes were isolated from six sampling sites at various stages and the 16S rRNA fragments were amplified with archaea-specific primers. Based on their rRNA sequences, a total of 180 clones, 30 clones from each site, could be divided into seven groups. Among them, group I to group V were assigned to the phylum Euryarchaeota, and group VI and group VII to the phylum Crenarchaeota. All the clones of group I (uncultured archaeon clone AE34) and group II (uncultured archaeon clone AS17) belonged to the class Methanomicrobia and the closest neighboring species was allocated to the Methanomicrobium mobile, a methanogen. Two major methanogen groups, I and II, were predominantly present at the initial stage and at the mid to late stages, respectively. The quantified values of their prevalence were 45.0% (81 out of a total of 180 clones) and 47.8% (86 of 180 clones), respectively. Group VI (an uncultured archaeon) and group VII (uncultured archaeon clone AF15) were minor groups and belonged to the class Thermoprotei. Little change in the methanogenic archaeal diversity was observed compared to that of the bacterial and fungal diversity. The results may help to gain information about CH₄ production from composting and to improve the fieldscale composter system, since the diversity would be dependent on the maturation and composition of the compost.