Industrial enzymes are produced by submerged fermentation (SF) and by solid-state fermentation (SSF) to a lesser extent. Although SSF has several advantages, its scale-up is difficult. The role of physiological and genetic properties of microorganisms growing attached to surfaces could explain the advantages of SSF. Filamentous fungi are naturally adapted to growth on surfaces and in these conditions they show a particular physiological behavior which is different from that in SF; thus, they also form biofilms. Fermentation by filamentous fungal biofilms (FFB) is a homogeneous production system within a liquid environment based on the infrastructure of the SF process with the productive efficiency of the SSF. Enzyme production levels of FFB are much higher than those obtained in SF and they are also amenable of mixed fungal cultivation. Transcriptomic and proteomic tools are used to uncover the fundamental biological issues behind FFB. Several genes encoding cellulolytic enzymes are either differentially expressed or overexpressed in FFB. Moreover, our proteomic studies of Aspergillus niger biofilms compared to SF indicate that many intracellular proteins are either differentially expressed or overexpressed. Clinically important fungi like A. fumigatus also form biofilms when they infect lungs and recent studies demonstrate same gene expression features. These results support our hypothesis of cell adhesion and its role in the new schemes for improved fermentative production of industrial enzymes.

Alkaline cellulase producing fungi were isolated from soils of an undisturbed rain forest of Peru. The soil dilution plate method was used for the enumeration and isolation of fast growing cellulolytic fungi on an enriched selective medium. Eleven out of 50 different morphological colonies were finally selected by using the plate clearing assay with CMC as substrate at different pH values. All 11 strains produced cellulases in liquid culture with activities at alkaline pH values without an apparent decrease of them indicating that they are true alkaline cellulase producers. Aspergillus sp. LM-HP32, Penicillium sp. LM-HP33, and Penicillium sp. LM-HP37 were the best producers of FP cellulase (>3 U mL−1) with higher specific productivities (>30 U g−1 h−1). Three strains have been found suitable for developing processes for alkaline cellulase production. Soils from Amazonian rain forests are good sources of industrial fungi with particular characteristics. The results of the present study are of commercial and biological interest. Alkaline cellulases may be used in the polishing and washing of denim processing of the textile industry.

Here, we report the complete genome sequence of a high alkaline cellulase producing Aspergillus fumigatus strain LMB-35Aa isolated from soil of Peruvian Amazon rainforest. The genome is ∼27.5mb in size, comprises of 228 scaffolds with an average GC content of 50%, and is predicted to contain a total of 8660 protein-coding genes. Of which, 6156 are with known function; it codes for 607 putative CAZymes families potentially involved in carbohydrate metabolism. Several important cellulose degrading genes, such as endoglucanase A, endoglucanase B, endoglucanase D and beta-glucosidase, are also identified. The genome of A. fumigatus strain LMB-35Aa represents the first whole sequenced genome of non-clinical, high cellulase producing A. fumigatus strain isolated from forest soil.

The textile industry creates environmental problems due to the release of highly polluting effluents containing substances from different stages of dyeing that are resistant to light, water, and various chemicals, and most of them are difficult to decolorize because of its synthetic origin. The biological degradation of dyes is an economical and environmentally friendly alternative. The aim of this work was to use biofilms of basidiomycete fungi isolated from the Peruvian rainforest for the decolorization of synthetic reactive dyes, considering the advantages of these systems which include better contact with the surrounding medium, resistance to chemical and physical stress, and higher metabolic activity. Among several isolates, two were selected for their capacity of rapid decolorization of several dyes and their biofilm-forming ability. These strains were molecularly identified as Trametes polyzona LMB-TM5 and Ceriporia sp. LMB-TM1 and used in biofilm cultivation for the decolorization of six reactive dyes and textile effluents. Azo dyes were moderately decolorized by both strains, but Remazol Brilliant Blue R (anthraquinone) and Synozol Turquoise Blue HF-G (phthalocyanine) were highly decolorized (97 and 80 %, respectively) by T. polyzona LMB-TM5. Degradation products were found by HPLC analysis. Simulated effluents made of a mixture of six dyes were moderately decolorized by both strains, but a real textile effluent was highly (93 %) decolorized by T. polyzona LMB-TM5. In summary, T. polyzona LMB-TM5 was more efficient than Ceriporia sp. LMB-TM1 for the decolorization of textile dyes and effluents at high initial rates enabling the development of in-plant continuous biofilm processes.

Filamentous fungus Aspergillus niger has high industrial value due to their lignocellulolytic enzyme activities and ATCC 10864 is one of the few type strains of A. niger which has a unique biofilm forming capability. Here we report the first draft genome sequence of A. niger ATCC 10864 strain. The genome of A. niger ATCC 10864 is 36,172,237 bp long and comprise of 310 scaffolds with 49.5% average GC content. A total of 10,804 protein-coding genes were predicted among which 10,761 genes were with putative functions. A. niger ATCC 10864 genome coded for 709 putative carbohydrate active enzyme families distributed in six functional categories and among them glycoside hydrolases (GHs) represent the most number of families (279). Genes that include pepA, brlA, exgA, LaeA, rodA, GCN have also been identified in this study, which may play a role in biofilm formation. This high-quality draft genome sequence will facilitate our understanding of the mechanisms behind fungal biofilm formation and higher lignocellulolytic enzyme production.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-017-0254-2) contains supplementary material, which is available to authorized users.