Isolation of cellulolytic enzymes from moldy silage by new culture-independent strategy

Exploring dynamics and associations of dominant lignocellulose degraders in tomato stalk composting

The plant residues of tomato bring pressures to the environment and composting provides a feasible method to treat such agricultural waste. However, little is known about the succession and associations of the dominant lignocellulose degraders in the compost system. To further accelerate the process by inoculating key functional microorganisms, a compost pile composed of tomato stalk with maize straw addition was constructed, and the whole community structure and functions of the dominant were investigated by applying the integrated mata-omics. Results showed that Actinobacteria, Firmicutes, and Ascomycota dominated and drove the assembly of the co-occurrence network. In the thermophilic stage, Thermobifida was the exclusive degrader of cellulose, and Thermobifida fusca was the most important cellulolytic actinomycete. Saccharomonospora viridis, Planifilum fulgidum, Thermobacillus sp. and the dominant ascomycota of Aspergillus sclerotialis participated in hemicellulose decomposing. In the cooling phase, functional microorganisms became more diverse, with Nocardiopsis flavescens, Glycomyces artemisiae, Glycomyces sambucus, Streptomyces rubrolavendulae and Streptomyces vietnamensis joining the cellulose-degrading rank, and Chaetomium thermophilum emerging as the main hemicellulose degrader. More than two thirds of the bacteria-bacteria interactions and all the fungi-fungi associations were positive, while, both competition (for the same substrate of hemicellulose) and synergy (preference for cellulose and hemicellulose) coexisted in the bacteria-fungi interactions. In conclusion, these findings provide useful information for understanding the biodegradation of tomato plant residues better, and effects of the functional agents identified on composting process should be further studied.

Enhanced Growth and Activities of the Dominant Functional Microbiota of Chicken Manure Composts in the Presence of Maize Straw

As a consequence of intensive feeding, the bulk deposition of livestock manure causes severe environmental problems. Composting is a promising method for waste disposal, and the fermentation process is driven by microbial communities. However, chicken manure contains diverse gut microbes, mainly species derived from Proteobacteria, which may include pathogens that threaten human health. To evaluate composting as a harmless treatment of livestock manure, the dynamics of the microbiota in two chicken manure composts were studied, and the influences of adding maize straw on the compost microbiota were compared. The results revealed that microbes from Firmicutes including Bacillus and Lentibacillus are the most dominant degraders with a strong amino acid metabolism, and they secrete a diverse array of proteases as revealed in metaproteomics data. The addition of maize straw to the chicken manure compost accelerated species succession at the initial stage, and stimulated carbohydrate metabolism in the dominant microbiota. Besides, under the resulting high temperature (>70°C) conditions, the relative abundance of Proteobacteria was reduced by 78% in composts containing maize straw by day 4, which was faster than in compost without added maize straw, in which the abundance was reduced by 66%. Adding maize straw to chicken manure composts can therefore increase the fermentation temperature and inhibit the growth of Proteobacteria. In general, these findings provide increased insight into the dynamic changes among the dominant functional microbiota in chicken manure composts, and may contribute to the optimization of livestock manure composting on an industrial scale.

Dynamic changes of the dominant functioning microbial community in the compost of a 90-m(3) aerobic solid state fermentor revealed by integrated meta-omics

The dynamic changes in the composition and function of both bacterial and fungal communities over time and at various depths in the compost of a 90-m(3) industrial-scale fermentor were explored using integrated meta-omics. The microbial communities in the middle layer (1.2m) of the compost developed a stable and simple structure over time, which was mainly composed of Thermobifida, Bacillus, Thermomyces and Aspergillus. According to the metaproteomic results, the bacterial community was more focused on cellulose degradation, characterized by 44% of the cellulases that were secreted by Thermobifida, while the fungal community was more likely to degrade hemicellulose, mainly via Thermomyces and Aspergillus. The results revealed that, under artificial control of the temperature and oxygen concentration, the efficiency of organic waste degradation was greatly increased and the fermentation cycle was shortened to 11 days.

Thermomyces lanuginosus is the dominant fungus in maize straw composts

The microbial community composition and function of three self-heating maize straw composts were compared by integrated meta-omics. The results revealed that the fungal communities were primarily dominated by the phylum Ascomycota (>90%) regardless of different nitrogen sources, which were exclusively composed of the Thermomyces, a genus of hemicellulose degraders. The bacterial community composition was affected by the addition of nitrogen sources, as the abundance of the Actinobacteria increased, while the Proteobacteria and Bacteroidetes decreased. Various hemicellulases and cellulases were detected in the composts, and the major xylanase secreted by Thermomyces lanuginosus was always present, revealing that it was the dominant fungus in hemicellulose hydrolysis and that bacteria and fungi might synergistically degrade lignocellulose. Thus, microbial communities in composts may develop a simple and stable structure of a dominant fungal species and limited numbers of bacterial species under the selective pressure of high temperature and maize straw as starting materials.

Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era

The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.

Mining metagenomes for novel cellulase genes

Cellulases hydrolyze the β-1,4 linkages of cellulose and are widely used in food, brewing and wine, animal feed, textiles and laundry, and pulp and paper industries, especially for hydrolyzing cellulosic materials into sugars, which can be fermented to produce useful products such as ethanol. Metagenomics has become an alternative approach to conventional culture-dependent methods as it allows exhaustive mining of microbial genomes in their natural environments. This review covers the current state of research and challenges in mining novel cellulase genes from the metagenomes of various environments, and discusses the potential biotechnological applications of metagenome-derived cellulases.