Regulation of fungal decomposition at single-cell level

Filamentous fungi play a key role as decomposers in Earth’s nutrient cycles. In soils, substrates are heterogeneously distributed in microenvironments. Hence, individual hyphae of a mycelium may experience very different environmental conditions simultaneously. In the current work, we investigated how fungi cope with local environmental variations at single-cell level. We developed a method based on infrared spectroscopy that allows the direct, in-situ chemical imaging of the decomposition activity of individual hyphal tips. Colonies of the ectomycorrhizal Basidiomycete Paxillus involutus were grown on liquid media, while parts of colonies were allowed to colonize lignin patches. Oxidative decomposition of lignin by individual hyphae growing under different conditions was followed for a period of seven days. We identified two sub-populations of hyphal tips: one with low decomposition activity and one with much higher activity. Active cells secreted more extracellular polymeric substances and oxidized lignin more strongly. The ratio of active to inactive hyphae strongly depended on the environmental conditions in lignin patches, but was further mediated by the decomposition activity of entire mycelia. Phenotypic heterogeneity occurring between genetically identical hyphal tips may be an important strategy for filamentous fungi to cope with heterogeneous and constantly changing soil environments.

[1]  Keith W. Goyne,et al.  Soil Chemical Insights Provided through Vibrational Spectroscopy , 2014 .

[2]  W. R. Whalley,et al.  Applications of X‐ray computed tomography for examining biophysical interactions and structural development in soil systems: a review , 2013 .

[3]  Romà Tauler,et al.  MCR-ALS GUI 2.0: New features and applications , 2015 .

[4]  S. Moukha,et al.  Localization of growth and secretion of proteins in Aspergillus niger. , 1991, Journal of general microbiology.

[5]  P. Markham,et al.  Woronin bodies of filamentous fungi , 1987 .

[6]  M. Hackett,et al.  Elemental and Chemically Specific X-ray Fluorescence Imaging of Biological Systems , 2014, Chemical reviews.

[7]  Damian P. Donnelly,et al.  Networks of power and influence: the role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning , 2004 .

[8]  Ingrid Kögel-Knabner,et al.  The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter , 2002 .

[9]  H. Flemming,et al.  The biofilm matrix , 2010, Nature Reviews Microbiology.

[10]  A. Schintlmeister,et al.  Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils , 2015, FEMS microbiology ecology.

[11]  W. Windig,et al.  Interactive self-modeling mixture analysis , 1991 .

[12]  A. Ram,et al.  Hyphal differentiation in the exploring mycelium of Aspergillus niger , 2005, Molecular microbiology.

[13]  G. Gadd The Geomycology of Elemental Cycling and Transformations in the Environment. , 2017, Microbiology spectrum.

[14]  A. Gutiérrez,et al.  Hyphal-sheath polysaccharides in fungal deterioration , 1995 .

[15]  G. Mie Beiträge zur Optik trüber Medien, speziell kolloidaler Metallösungen , 1908 .

[16]  J. Chalmers Mid-Infrared Spectroscopy: Anomalies, Artifacts and Common Errors , 2006 .

[17]  A. Tunlid,et al.  The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus , 2013, The New phytologist.

[18]  Marcel J. T. Reinders,et al.  Switching from a Unicellular to Multicellular Organization in an Aspergillus niger Hypha , 2015, mBio.

[19]  Rohit Bhargava,et al.  Using Fourier transform IR spectroscopy to analyze biological materials , 2014, Nature Protocols.

[20]  Lynne Boddy,et al.  SAPROTROPHIC CORD-FORMING FUNGI : MEETING THE CHALLENGE OF HETEROGENEOUS ENVIRONMENTS , 1999 .

[21]  F. Watteau,et al.  Soil Microstructures Examined Through Transmission Electron Microscopy Reveal Soil-Microorganisms Interactions , 2018, Front. Environ. Sci..

[22]  A. Gladfelter,et al.  Nuclear autonomy in multinucleate fungi. , 2015, Current opinion in microbiology.

[23]  K. Ruel,et al.  Involvement of an Extracellular Glucan Sheath during Degradation of Populus Wood by Phanerochaete chrysosporium , 1991, Applied and environmental microbiology.

[24]  Lynne Boddy,et al.  The Mycelium as a Network. , 2017, Microbiology spectrum.

[25]  Katsuhiko Kitamoto,et al.  Hyphal heterogeneity in Aspergillus oryzae is the result of dynamic closure of septa by Woronin bodies , 2012, Molecular microbiology.

[26]  D. Sparks,et al.  Advances in Scanning Transmission X-Ray Microscopy for Elucidating Soil Biogeochemical Processes at the Submicron Scale. , 2017, Journal of environmental quality.

[27]  P. Persson,et al.  Desorption mechanisms of phosphate from ferrihydrite and goethite surfaces , 2016 .

[28]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[29]  B. Lindahl,et al.  Ectomycorrhizal fungi - potential organic matter decomposers, yet not saprotrophs. , 2015, The New phytologist.

[30]  T. Breit,et al.  Single cell transcriptomics of neighboring hyphae of Aspergillus niger , 2011, Genome Biology.

[31]  J. Wessels Tansley Review No. 45 Wall growth, protein excretion and morphogenesis in fungi. , 1993, The New phytologist.

[32]  C. Troein,et al.  The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen , 2018, The ISME Journal.

[33]  O. Faix,et al.  Classification of Lignins from Different Botanical Origins by FT-IR Spectroscopy , 1991 .

[34]  A. Barth Infrared spectroscopy of proteins. , 2007, Biochimica et biophysica acta.

[35]  D. Marion,et al.  Increased endoplasmic reticulum content of Phanerochaete chrysosporium INA-12 by inositol phospholipid precursor in relation to peroxidase excretion , 1991, Applied Microbiology and Biotechnology.

[36]  Barbara H. Stuart,et al.  Infrared Spectroscopy: Fundamentals and Applications: Stuart/Infrared Spectroscopy: Fundamentals and Applications , 2005 .

[37]  Claire E. Stanley,et al.  Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae , 2019, Current Biology.

[38]  I. Kögel‐Knabner The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter: Fourteen years on , 2017 .

[39]  R. D. de Vries,et al.  Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies. , 2011, Environmental microbiology.

[40]  L Boddy,et al.  Imaging complex nutrient dynamics in mycelial networks , 2008, Journal of microscopy.

[41]  N. Fries Basidiospore germination in some mycorrhiza-forming hymenomycetes , 1978 .

[42]  O. Monga,et al.  Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain , 2018, Front. Microbiol..

[43]  S. West,et al.  Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks , 2019, Current Biology.

[44]  C. Peterson,et al.  Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus , 2018, The New phytologist.

[45]  R. D. de Vries,et al.  Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass. , 2015, Advances in applied microbiology.

[46]  Simple-to-use interactive self-modeling mixture analysis of FTIR microscopy data , 1993 .

[47]  H. Wösten,et al.  In situ hybridisation in filamentous fungi using peptide nucleic acid probes. , 2004, Fungal genetics and biology : FG & B.

[48]  Jerome T. Mettetal,et al.  Stochastic switching as a survival strategy in fluctuating environments , 2008, Nature Genetics.

[49]  Martin Ackermann,et al.  A functional perspective on phenotypic heterogeneity in microorganisms , 2015, Nature Reviews Microbiology.

[50]  T. Eickhorst,et al.  Correlative Imaging Reveals Holistic View of Soil Microenvironments. , 2018, Environmental science & technology.

[51]  J. Jellison,et al.  Fungal variegatic acid and extracellular polysaccharides promote the site-specific generation of reactive oxygen species , 2017, Journal of Industrial Microbiology & Biotechnology.

[52]  Alexander F Routh,et al.  Drying of thin colloidal films , 2013, Reports on progress in physics. Physical Society.

[53]  Norio Takeshita Oscillatory fungal cell growth. , 2018, Fungal genetics and biology : FG & B.

[54]  Paul Dumas,et al.  Resonant Mie scattering in infrared spectroscopy of biological materials--understanding the 'dispersion artefact'. , 2009, The Analyst.

[55]  M. Fricker,et al.  Emergence of self-organised oscillatory domains in fungal mycelia. , 2007, Fungal genetics and biology : FG & B.

[56]  C. Bledsoe,et al.  Nitrogen Transfer Within and Between Plants Through Common Mycorrhizal Networks (CMNs) , 2003 .

[57]  K. Hammel,,et al.  Fungal Biodegradation of Lignocelluloses , 2011 .

[58]  P. Lasch,et al.  Spatial resolution in infrared microspectroscopic imaging of tissues. , 2006, Biochimica et biophysica acta.

[59]  E. Lindquist,et al.  The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry , 2012, Environmental microbiology.