Table 2.
Dominant bacterial communities in different types of substrates.
| Substrate Types | Dominant Bacteria | Properties Related to the Cultivation | Method of Analysis | Mushroom | References | |
|---|---|---|---|---|---|---|
| Phylum | Class/Order/Genus | |||||
| Wheat straw-based compost | Proteobacteria | Pseudoxanthomonas | Cellulose-degrading consortium | DGGE and T-RFLP analysis |
A. bisporus | [12] |
| Actinobacteria | Thermobifida Thermomonospora | |||||
| Corncob compost (Early stage) |
Firmicutes | Carnobacterium | - | Metagenomic sequencing | P. ostreatus | [15] |
| Proteobacteria | Pseudomonas Stenotrophomonas | |||||
| Bacteroidetes | Sphingobacterium | |||||
| Actinobacteria | Glutamicibacter | |||||
| Corncob compost (Thermophilic stage) |
Firmicutes | Aerococcus | - | |||
| Bacillus | ||||||
| Desemzia | ||||||
| Lysinibacillus | ||||||
| Enterococcus | ||||||
| Proteobacteria | Acinetobacter | |||||
| Actinobacteria | Corynebacterium | |||||
| Naturally occurring soil and mushroom | Acidobacteria | - | - | DNA sequencing | C. militaris | [16] |
| Actinobacteria | ||||||
| Bacteroidetes Proteobacteria | ||||||
| Soil in fruiting body | Firmicutes | - | - | 16 rRNA amplicons, Illumina MiSeq sequencing |
O. highlandensis | [17] |
| Verrucomicrobia | ||||||
| Deltaproteobacteria | ||||||
| Proteobacteria | ||||||
| Peach sawdust-based compost | Firmicutes | - | - | Metagenomic 16S rRNA sequencing | Oyster mushroom | [80] |
| Actinobacteria | ||||||
| Proteobacteria | ||||||
| Compost | Thermodesulfobacteria | Thermodesulfobacterium | Sulfur-reducing properties | DNA and cDNA sequencing | A. bisporus | [92] |
| Proteobacteria | Pseudoxanthomonas | |||||
| Actinobacteria | - | |||||
| Firmicutes | - | |||||
| Natural composting samples (Mesophilic stage) |
Actinobacteria | Actinomycetales Bacillales Clostridiales |
- | DNA sequence with Roche/454 technology | - | [135] |
| Firmicutes |
Rhodococcus
Lactobacillus Thermobifida |
- | ||||
| Actinobacteria | Amycolatopsis | Potential for lignin degradation | ||||
| Maize straw compost | Firmicutes |
Sporosarcina
Bacillus Staphylococcus |
- | Illumina MiSeq sequencing | - | [151] |
| Proteobacteria |
Pseudomonas
Ochrobactrum |
- | ||||
| Bacteroidetes | - | - | ||||
| Actinobacteria | Cellulosimicrobium | Produce lignocellulose hydrolytic enzymes | ||||
| Sugarcane processing | Firmicutes | Bacillales Lactobacillales Clostridiales |
Fermentation | PhyloChip microarray | - | [152] |
| Proteobacteria | - | - | ||||
| Bacteroidetes | - | - | ||||
| Wood chips and sawdust compost | Actinobacteria | Brevibacterium | Degrade cellulose | Real-time PCR and DGGE | - | [153] |
| Micrococcineae | Degrade lignocellulosic materials |
|||||
| Cellulomonas | Produce cellulases and hemicellulases | |||||
| Composting from waste management system | Actinobacteria | - | - | DNA sequencing | - | [154] |
| Bacteroidetes | - | - | ||||
| Firmicutes | Bacillus | Produce proteases | ||||
| Clostridium | Degrade cellulose and lignin | |||||
| Lactobacillus | Related to low pH | |||||
| Thermoactinomyces | - | |||||
| Proteobacteria | Acetobacter | Related to low pH | ||||
| Deinococcus-Thermus | - | - | ||||
(-) = not determined in the reference.