Fungal biofilm morphology impacts hypoxia fitness and disease progression


Microbial populations form intricate macroscopic colonies with diverse morphologies whose functions remain to be fully understood. Despite fungal colonies isolated from environmental and clinical samples revealing abundant intraspecies morphological diversity, it is unclear how this diversity affects fungal fitness and disease progression. Here we observe a notable effect of oxygen tension on the macroscopic and biofilm morphotypes of the human fungal pathogen Aspergillus fumigatus. A hypoxia-typic morphotype is generated through the expression of a subtelomeric gene cluster containing genes that alter the hyphal surface and perturb interhyphal interactions to disrupt in vivo biofilm and infection site morphologies. Consequently, this morphotype leads to increased host inflammation, rapid disease progression and mortality in a murine model of invasive aspergillosis. Taken together, these data suggest that filamentous fungal biofilm morphology affects fungal–host interactions and should be taken into consideration when assessing virulence and host disease progression of an isolated strain.

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Fig. 1: Macroscopic morphotypes and biofilm architecture of A. fumigatus are influenced by oxygen tension.
Fig. 2: The hypoxia-evolved allele of the subtelomeric gene hrmA is sufficient to generate H-MORPH and collapse biofilm architecture.
Fig. 3: Transcriptional rewiring of the hypoxia response is dependent on the hypoxia-evolved allele of hrmA and primes for improved growth in low oxygen.
Fig. 4: HrmA localizes to the nucleus where it facilitates induction of a subtelomeric gene cluster.
Fig. 5: HrmA-facilitated induction of the surrounding subtelomeric gene cluster leads to increased hypoxia fitness and a modified hyphal surface.
Fig. 6: H-MORPH contributes to increased virulence through increased inflammation and diffuse lesion morphology.

Data availability

RNA sequencing data that support the findings of this study have been deposited under NCBI Gene Expression Omnibus with the identifier GSE133440 under the BioProject PRJNA551460. The genomic sequencing data for EVOL20 and reference AF293 have been deposited under BioProject identifier PRJNA417720. All strains and any other data used to support these findings will be made available upon reasonable request to the corresponding author.

Code availability

The custom scripts that were used in this study are available at,, and The BiofilmQ software is available for public download at Other data that support the findings presented here are available upon request from the corresponding author.


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We thank J. Obar (Dartmouth) for his helpful comments, A. Lavanway and L. Howard (Dartmouth) for their microscopy expertise, T. J. Smith for graphical model design and construction, D. Limoli for funPACT assistance, S. Dhingra for tool development (plasmids), D. Carter-House for assistance with DNA extraction for whole genome sequencing and S. Lockhart, S. Howard, and D. Hagiwara for sharing A. fumigatus isolates. This work was supported by the efforts of R.A.C. through funding by NIH National Institute of Allergy and Infectious Diseases (NIAID) (grant nos. R01AI130128 and 2R01AI081838). R.A.C holds an Investigators in Pathogenesis of Infectious Diseases Award from the Burroughs Wellcome Fund. C.H.K. was supported by the Molecular and Cellular Biology Training Grant at Dartmouth (no. 5T32 GM 8704-20, principal investigator: D. Compton) from the National Institute of General Medical Sciences from July 2016 to June 2018 and the NIH NIAID Ruth L. Kirschstein National Research Service Award (no. F31AI138354) from July 2018. C.D.N. is supported by the National Science Foundation (grant no. MCB 1817342), a Burke Award from Dartmouth College, a pilot award from the Cystic Fibrosis Foundation (grant no. STANTO15RO) and NIH grant no. P20-GM113132 to the Dartmouth BioMT COBRE. Data analyses were performed on the UC Riverside High-Performance Computational Cluster supported by grant nos. NSF DBI-1429826 and NIH S10-OD016290.

Author information




C.H.K. designed, performed and analysed most of the experiments and wrote the manuscript. J.D.K. performed the histopathology quantification and assisted with funPact analysis. K.L. performed the cellularity analysis. M.C.B. assisted with fluorescent microscopy analysis. R.H. generated software for biofilm analysis. C.D.N. generated software for biofilm analysis and performed the biofilm analysis. J.E.S. performed analysis on genomic and RNA sequencing and phylogenetic analysis. R.A.C. designed experiments, supervised the study and edited the manuscript. All authors reviewed and approved the manuscript.

Corresponding author

Correspondence to Robert A. Cramer.

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Supplementary information

AF293 biofilm at 21% O2.

AF293 biofilm at 0.2%.

EVOL20 biofilm at 21% O2.

EVOL20 biofilm at 0.2% O2.

funPACT, AF293, lesion, day 5 post inoculation.

funPACT, EVOL20, lesion day 5 post inoculation.

Supplementary Information

Supplementary Figs. 1–16, video legends, methods and references.

Reporting Summary

Supplementary Tables

Supplementary Tables 1–9

Supplementary Video 1

AF293 biofilm at 21% O2.

Supplementary Video 2

AF293 biofilm at 0.2%.

Supplementary Video 3

EVOL20 biofilm at 21% O2.

Supplementary Video 4

EVOL20 biofilm at 0.2% O2.

Supplementary Video 5

funPACT, AF293, lesion, day 5 post inoculation.

Supplementary Video 6

funPACT, EVOL20, lesion day 5 post inoculation.

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Kowalski, C.H., Kerkaert, J.D., Liu, K. et al. Fungal biofilm morphology impacts hypoxia fitness and disease progression. Nat Microbiol 4, 2430–2441 (2019).

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