Succession of physiological stages hallmarks the transcriptomic response of the\xa0fungus Aspergillus niger to lignocellulose

Jolanda M Van Munster ,Erika Lindquist,Matt Kokolski,Young-Mo Kim ,Steven T Pullan ,Blake A Simmons ,Leanne Jade G Chan ,Martin Blythe ,Roger Ibbett,Gregory A Tucker ,Kerrie Barry ,Mikko Arvas,Paul Daly,Roxane Raulo,Igor V Grigoriev ,Anna Lipzen,Vasanth Singan ,Sanyasi Gaddipati,Stéphane Delmas,Chew Yee Ngan,David B Archer

doi:10.1186/s13068-020-01702-2

Abstract

BackgroundUnderstanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production.ResultsWe analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds.ConclusionIn this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.

Highlights

Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes
Aspergillus niger cultivation over time is affected by pretreatment of Miscanthus that influences its composition and digestibility Aspergillus niger was exposed to knife-milled Miscanthus (KMM) as well as ionic liquid (IL) and hydrothermally (HT) pretreated Miscanthus for up to 5 days to identify the system-level fungal responses upon exposure to these substrates (Fig. 1a)
The xylan detected in the solid fraction retrieved from cultures of A. niger with KMM reduced by 26% over the first 24 h of cultivation, whereas in HT pretreated Miscanthus (HTM) it reduced by only 18%, suggesting less degradation of HTM than KMM during cultivations (Additional file 1: Fig. S1d)

Summary

Introduction

Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Industrial scale use of plant biomass for biotechnologies is hampered by biomass recalcitrance [5, 6], whereas nature evolved effective microbial systems to recycle lignocellulose [7,8,9]. Through tightly regulated responses to nutritional and environmental cues they can secrete a large array of hydrolytic enzymes and other effectors [7, 13,14,15,16,17] Fungi such as Trichoderma reesei and Aspergillus niger are widely used in commercial production of these enzymes, due to their high titer secretion of degradative enzymes under industrial conditions [18, 19]. It is imperative to increase the understanding of the saprotrophic biology of these particular fungi

Objectives

Methods

Results

Conclusion