DGGE and T-RFLP Analysis of Bacterial Succession during Mushroom Compost Production and Sequence-aided T-RFLP Profile of Mature Compost

Abstract

The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora.

Bacterial community changes during composting of municipal crop waste using low technology methods as revealed by 16S rRNA

“…Temperatures are usually high in the tropics, which increases evaporation of moisture from compost when it is not covered. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Planctomycetes which were the dominant phyla have been reported in other composting studies (Takaku et al, 2006;Danon et al, 2008;Székely et al, 2008;Vivas et al, 2009;Neher et al 2013;Karadag et al, 2013;Song et al, 2014;Manyl-loh et al. 2016).…”

Diversity and seasonal dynamics of the photoautotrophic picoplankton in Lake Balaton (Hungary)

“…compared with sequence-aided terminal restriction fragment length polymorphism [T-RFLP], it lacks the requirement for restriction digestion of amplified genomic DNA; e.g. Székely et al 2008, Felföldi et al 2010. Because all stages in molecular biological approaches may introduce significant biases (Wintzingerode et al 1997, Sipos et al 2007, methods with fewer stages should have a less distorting effect on the original community structure.…”

Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for Agaricus bisporus production

“…However, limited information is available regarding the microbiology of the specific composting methodology used to produce compost for the cultivation of A. bisporus [37]. Furthermore, this lack of knowledge is particularly pronounced for Phase I composting, as this process occurs more slowly and is less well-regulated than Phase II, which requires only a relatively short indoor heat treatment (pasteurization) to prepare a pathogen-free and selective mushroom growth substrate [27].…”