Objective  The integrated meta-omics was applied to reveal the functional microorganisms in the tomato stalks/maize straws compost.

  Method  Sampling from the pile of a compost of tomato stalks and maize straws in the ratio of 3:1 (m: m) at the height of 20–50 cm was carried out once every week for lignocellulosic enzyme assay. When a peak enzymatic activity appeared, specimens were collected and the integrated meta-omic analysis that combined high-throughput pyrosequencing and Orbitrap studies was conducted.

  Result  The greatest population of fungi in the compost belonged to the phylum Ascomycota, in which, Thermomyces was the most abundant accounting for 70.5%. Thermomyces is known to secret endo-1,4-β-xylanase that degrades hemicellulose in biomass. Of the total bacteria population, Actinobacteria, Proteobacteria, and Firmicutes phyla made up 87.0%, and the two genera of Actinobacteria, Thermobifida and Saccharomonospora, accounted for 16.5% and 1.36%, respectively. Thermobifida is capable of degrading cellulose with its 4 endoglucanases and 3 cellobiohydrolases. It also secrets enzymes associated with hemicellulose and pectate degradation. Saccharomonospora produces a β-xylanase, 2 serine proteases and 2 trypsins involved in the decomposition of hemicelluloses and proteins. Idiomarina was the major genus of Proteobacteria found in the compost with a relative abundance of 15.6%. It involves in protein degradation. Although low in abundance (merely 1.23%), Planifilum of Firmicutes phylum plays an import role in degrading hemicelluloses.

  Conclusion  The integrated meta-omics that combined pyrosequencing and Orbitrap analysis provided a new tool for studying the community structure and functions of the microorganisms in a complex habitat such as a compost of different bio-materials. With the information obtained, ways to accelerate the composting process could be explored.