Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

doi:10.1111/1462-2920.14907

Title: Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Abstract

Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network ofbranching and fusing hyphae that are often considered to be relatively uniform entities inwhich nutrients can freely move through the hyphae. In nature, different parts of a colony areoften exposed to different nutrients. We have investigated, using a multi-omics approach,adaptation of A. niger colonies to spatially separated and compositionally different plantbiomass substrates. This demonstrated a high level of intra-colony differentiation, whichclosely matched the locally available substrate. The part of the colony exposed to pectin-richsugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytictranscript and protein levels, respectively.This study therefore exemplifies the high ability of fungal colonies to differentiate and adaptto local conditions, ensuring efficient use of the available nutrients, rather than maintaining auniform physiology throughout the colony.

Authors:

Daly, Paul ^[1]; Peng, Mao ^[1]; Mitchell, Hugh D. ^[2];

^[2]; Ansong, Charles K. ^[2];

^[2]; De Gijsel, Peter ^[3];

^[2]; Markillie, Lye Meng ^[2];

^[2];

^[2]; Wiebenga, Ad ^[1]; Hilden, Kristiina S. ^[4]; Kabel, Mirjam A. ^[3];

^[2]; Makela, Miia ^[4]; De Vries, Ronald P. ^[4]

Univ. of Utrecht (Netherlands)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Wageningen Univ. (The Netherlands)
Univ. of Helsinki (Finland)

Publication Date:: 2019-08-06

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1604781

Report Number(s):: PNNL-SA-150305
Journal ID: ISSN 1462-2912

Grant/Contract Number:: AC05-76RL01830

Resource Type:: Accepted Manuscript

Journal Name:: Environmental Microbiology

Additional Journal Information:: Journal Volume: 22; Journal Issue: 3; Journal ID: ISSN 1462-2912

Publisher:: Wiley

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Daly, Paul, Peng, Mao, Mitchell, Hugh D., Kim, Young-Mo, Ansong, Charles K., Brewer, Heather M., De Gijsel, Peter, Lipton, Mary S., Markillie, Lye Meng, Nicora, Carrie D., Orr, Galya, Wiebenga, Ad, Hilden, Kristiina S., Kabel, Mirjam A., Baker, Scott E., Makela, Miia, and De Vries, Ronald P. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation.  United States: N. p., 2019. 
        Web.  doi:10.1111/1462-2920.14907.

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                    Daly, Paul, Peng, Mao, Mitchell, Hugh D., Kim, Young-Mo, Ansong, Charles K., Brewer, Heather M., De Gijsel, Peter, Lipton, Mary S., Markillie, Lye Meng, Nicora, Carrie D., Orr, Galya, Wiebenga, Ad, Hilden, Kristiina S., Kabel, Mirjam A., Baker, Scott E., Makela, Miia, & De Vries, Ronald P. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation.  United States.  doi:https://doi.org/10.1111/1462-2920.14907

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                    Daly, Paul, Peng, Mao, Mitchell, Hugh D., Kim, Young-Mo, Ansong, Charles K., Brewer, Heather M., De Gijsel, Peter, Lipton, Mary S., Markillie, Lye Meng, Nicora, Carrie D., Orr, Galya, Wiebenga, Ad, Hilden, Kristiina S., Kabel, Mirjam A., Baker, Scott E., Makela, Miia, and De Vries, Ronald P. Tue .  
        "Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation".  United States.  doi:https://doi.org/10.1111/1462-2920.14907.  https://www.osti.gov/servlets/purl/1604781.

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@article{osti_1604781,

  title        = {Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation},

  author       = {Daly, Paul and Peng, Mao and Mitchell, Hugh D. and Kim, Young-Mo and Ansong, Charles K. and Brewer, Heather M. and De Gijsel, Peter and Lipton, Mary S. and Markillie, Lye Meng and Nicora, Carrie D. and Orr, Galya and Wiebenga, Ad and Hilden, Kristiina S. and Kabel, Mirjam A. and Baker, Scott E. and Makela, Miia and De Vries, Ronald P.},

  abstractNote = {Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network ofbranching and fusing hyphae that are often considered to be relatively uniform entities inwhich nutrients can freely move through the hyphae. In nature, different parts of a colony areoften exposed to different nutrients. We have investigated, using a multi-omics approach,adaptation of A. niger colonies to spatially separated and compositionally different plantbiomass substrates. This demonstrated a high level of intra-colony differentiation, whichclosely matched the locally available substrate. The part of the colony exposed to pectin-richsugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytictranscript and protein levels, respectively.This study therefore exemplifies the high ability of fungal colonies to differentiate and adaptto local conditions, ensuring efficient use of the available nutrients, rather than maintaining auniform physiology throughout the colony.},

  doi          = {10.1111/1462-2920.14907},

  journal      = {Environmental Microbiology},

  number       = 3,

  volume       = 22,

  place        = {United States},

  year         = {2019},

  month        = {8}

}

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DOI: https://doi.org/10.1111/1462-2920.14907

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Works referenced in this record:

MetaboAnalyst 3.0—making metabolomics more meaningful
journal, April 2015

Xia, Jianguo; Sinelnikov, Igor V.; Han, Beomsoo
Nucleic Acids Research, Vol. 43, Issue W1
DOI: 10.1093/nar/gkv380

Woronin body-based sealing of septal pores
journal, December 2017

Steinberg, Gero; Harmer, Nicholas J.; Schuster, Martin
Fungal Genetics and Biology, Vol. 109
DOI: 10.1016/j.fgb.2017.10.006

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus
journal, January 2013

Patyshakuliyeva, Aleksandrina; Jurak, Edita; Kohler, Annegret
BMC Genomics, Vol. 14, Issue 1
DOI: 10.1186/1471-2164-14-663

DAnTE: a statistical tool for quantitative analysis of -omics data
journal, May 2008

Polpitiya, A. D.; Qian, W. -J.; Jaitly, N.
Bioinformatics, Vol. 24, Issue 13
DOI: 10.1093/bioinformatics/btn217

How does a hypha grow? The biophysics of pressurized growth in fungi
journal, June 2011

Lew, Roger R.
Nature Reviews Microbiology, Vol. 9, Issue 7
DOI: 10.1038/nrmicro2591

A broader role for AmyR in Aspergillus niger: regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides
journal, August 2011

vanKuyk, Patricia A.; Benen, Jaques A. E.; Wösten, Han A. B.
Applied Microbiology and Biotechnology, Vol. 93, Issue 1
DOI: 10.1007/s00253-011-3550-6

Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae
journal, January 2019

Schmieder, Stefanie S.; Stanley, Claire E.; Rzepiela, Andrzej
Current Biology, Vol. 29, Issue 2
DOI: 10.1016/j.cub.2018.11.058

NCBI GEO: archive for functional genomics data sets—update
journal, November 2012

Barrett, Tanya; Wilhite, Stephen E.; Ledoux, Pierre
Nucleic Acids Research, Vol. 41, Issue D1
DOI: 10.1093/nar/gks1193

Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin
journal, September 2017

Kowalczyk, Joanna E.; Lubbers, Ronnie J. M.; Peng, Mao
Scientific Reports, Vol. 7, Issue 1
DOI: 10.1038/s41598-017-12362-y

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood : Responses of
journal, October 2018

Daly, Paul; López, Sara Casado; Peng, Mao
Environmental Microbiology, Vol. 20, Issue 11
DOI: 10.1111/1462-2920.14416

The Structure and Function of the Vegetative Mycelium of Ectomycorrhizal Plants. i. Translocation of 14c-Labelled Carbon Between Plants Interconnected by a Common Mycelium
journal, May 1986

Finlay, R. D.; Read, D. J.
New Phytologist, Vol. 103, Issue 1
DOI: 10.1111/j.1469-8137.1986.tb00603.x

A new self-assembled peroxisomal vesicle required for efficient resealing of the plasma membrane
journal, March 2000

Jedd, Gregory; Chua, Nam-Hai
Nature Cell Biology, Vol. 2, Issue 4
DOI: 10.1038/35008652

Physiological Significance of Network Organization in Fungi
journal, September 2012

Simonin, Anna; Palma-Guerrero, Javier; Fricker, Mark
Eukaryotic Cell, Vol. 11, Issue 11
DOI: 10.1128/EC.00213-12

Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry
journal, November 2006

Kelly, Ryan T.; Page, Jason S.; Luo, Quanzhou
Analytical Chemistry, Vol. 78, Issue 22, p. 7796-7801
DOI: 10.1021/ac061133r

FactoMineR : An R Package for Multivariate Analysis
journal, January 2008

Lê, Sébastien; Josse, Julie; Husson, François
Journal of Statistical Software, Vol. 25, Issue 1
DOI: 10.18637/jss.v025.i01

Biological solutions to transport network design
journal, July 2007

Bebber, Daniel P.; Hynes, Juliet; Darrah, Peter R.
Proceedings of the Royal Society B: Biological Sciences, Vol. 274, Issue 1623
DOI: 10.1098/rspb.2007.0459

Mycelial density profiles of fungi on heterogeneous media and their interpretation in terms of nutrient reallocation patterns
journal, February 1995

Olsson, Stefan
Mycological Research, Vol. 99, Issue 2
DOI: 10.1016/S0953-7562(09)80878-2

Posttranscriptional Control of Gene Expression in Filamentous Fungi
journal, March 1998

Sachs, Matthew S.
Fungal Genetics and Biology, Vol. 23, Issue 2
DOI: 10.1006/fgbi.1998.1041

Quantification of Lignin and Its Structural Features in Plant Biomass Using ¹³ C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS
journal, October 2017

van Erven, Gijs; de Visser, Ries; Merkx, Donny W. H.
Analytical Chemistry, Vol. 89, Issue 20
DOI: 10.1021/acs.analchem.7b02632

Genetic analysis and the construction of master strains for assignment of genes to six linkage groups in Aspergillus niger
journal, November 1988

Bos, C. J.; Debets, A. J. M.; Swart, K.
Current Genetics, Vol. 14, Issue 5
DOI: 10.1007/BF00521266

Switching from a Unicellular to Multicellular Organization in an Aspergillus niger Hypha
journal, March 2015

Bleichrodt, Robert-Jan; Hulsman, Marc; Wösten, Han A. B.
mBio, Vol. 6, Issue 2
DOI: 10.1128/mBio.00111-15

Fungal enzyme sets for plant polysaccharide degradation
journal, July 2011

van den Brink, Joost; de Vries, Ronald P.
Applied Microbiology and Biotechnology, Vol. 91, Issue 6, p. 1477-1492
DOI: 10.1007/s00253-011-3473-2

Localization of growth and secretion of proteins in Aspergillus niger
journal, August 1991

Wosten, H. A. B.; Moukha, S. M.; Sietsma, J. H.
Journal of General Microbiology, Vol. 137, Issue 8
DOI: 10.1099/00221287-137-8-2017

Analysis of fungal networks
journal, April 2012

Heaton, Luke; Obara, Boguslaw; Grau, Vincente
Fungal Biology Reviews, Vol. 26, Issue 1
DOI: 10.1016/j.fbr.2012.02.001

Aiming for the complete utilization of sugar-beet pulp: Examination of the effects of mild acid and hydrothermal pretreatment followed by enzymatic digestion
journal, January 2011

Kühnel, Stefan; Schols, Henk A.; Gruppen, Harry
Biotechnology for Biofuels, Vol. 4, Issue 1
DOI: 10.1186/1754-6834-4-14

A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics
journal, August 2011

Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.
Analytical Chemistry, Vol. 83, Issue 16
DOI: 10.1021/ac2009806

Simplified method for the measurement of total non-starch polysaccharides by gas-liquid chromatography of constituent sugars as alditol acetates
journal, January 1984

Englyst, Hans N.; Cummings, John H.
The Analyst, Vol. 109, Issue 7
DOI: 10.1039/an9840900937

Direct transfer of carbon between plants connected by vesicular–arbuscular mycorrhizal mycelium
journal, January 1984

Francis, R.; Read, D. J.
Nature, Vol. 307, Issue 5946
DOI: 10.1038/307053a0

Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics
journal, March 2009

Martens-Uzunova, Elena S.; Schaap, Peter J.
Fungal Genetics and Biology, Vol. 46, Issue 1
DOI: 10.1016/j.fgb.2008.07.021

Advances in proteomics data analysis and display using an accurate mass and time tag approach
journal, January 2006

Zimmer, Jennifer S. D.; Monroe, Matthew E.; Qian, Wei-Jun
Mass Spectrometry Reviews, Vol. 25, Issue 3
DOI: 10.1002/mas.20071

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization
journal, August 2015

Benoit, Isabelle; Zhou, Miaomiao; Vivas Duarte, Alexandra
Scientific Reports, Vol. 5, Issue 1
DOI: 10.1038/srep13592

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger
journal, November 2017

Gruben, Birgit S.; Mäkelä, Miia R.; Kowalczyk, Joanna E.
BMC Genomics, Vol. 18, Issue 1
DOI: 10.1186/s12864-017-4164-x

Isolation of Aspergillus niger creA mutants and effects of the mutations on expression of arabinases and L-arabinose catabolic enzymes
journal, September 1997

Ruijter, G. J. G.; Vanhanen, S. A.; Gielkens, M. M. C.
Microbiology, Vol. 143, Issue 9
DOI: 10.1099/00221287-143-9-2991

HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014

Anders, S.; Pyl, P. T.; Huber, W.
Bioinformatics, Vol. 31, Issue 2
DOI: 10.1093/bioinformatics/btu638

Hyphal homing, fusion and mycelial interconnectedness
journal, March 2004

Glass, N.
Trends in Microbiology, Vol. 12, Issue 3
DOI: 10.1016/j.tim.2004.01.007

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
Nucleic Acids Research, Vol. 42, Issue D1
DOI: 10.1093/nar/gkt1178

2016 update of the PRIDE database and its related tools
journal, November 2015

Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi
Nucleic Acids Research, Vol. 44, Issue D1
DOI: 10.1093/nar/gkv1145

Cytoplasmic Continuity Revisited: Closure of Septa of the Filamentous Fungus Schizophyllum commune in Response to Environmental Conditions
journal, June 2009

van Peer, Arend F.; Müller, Wally H.; Boekhout, Teun
PLoS ONE, Vol. 4, Issue 6
DOI: 10.1371/journal.pone.0005977

Expression profiling of pectinolytic genes from Aspergillus niger
journal, September 2002

de Vries, Ronald P.; Jansen, Jenny; Aguilar, Guillermo
FEBS Letters, Vol. 530, Issue 1-3
DOI: 10.1016/S0014-5793(02)03391-4

Spatial Differentiation in the Vegetative Mycelium of Aspergillus niger
journal, October 2007

Levin, Ana M.; de Vries, Ronald P.; Conesa, Ana
Eukaryotic Cell, Vol. 6, Issue 12
DOI: 10.1128/EC.00244-07

Aspergillus Enzymes Involved in Degradation of Plant Cell Wall Polysaccharides
journal, December 2001

de Vries, R. P.; Visser, J.
Microbiology and Molecular Biology Reviews, Vol. 65, Issue 4
DOI: 10.1128/MMBR.65.4.497-522.2001

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass
journal, August 2015

Benoit, Isabelle; Culleton, Helena; Zhou, Miaomiao
Biotechnology for Biofuels, Vol. 8, Issue 1
DOI: 10.1186/s13068-015-0285-0

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification
journal, December 2016

Mäkelä, Miia R.; Mansouri, Sadegh; Wiebenga, Ad
New Biotechnology, Vol. 33, Issue 6
DOI: 10.1016/j.nbt.2016.07.014

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
journal, January 2007

Pel, Herman J.; de Winde, Johannes H.; Archer, David B.
Nature Biotechnology, Vol. 25, Issue 2, p. 221-231
DOI: 10.1038/nbt1282

Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon
journal, April 2003

Ferguson, B. A.; Dreisbach, T. A.; Parks, C. G.
Canadian Journal of Forest Research, Vol. 33, Issue 4
DOI: 10.1139/x03-065

Wheat Bran Proteins: A Review of Their Uses and Potential
journal, February 2015

Balandrán-Quintana, René Renato; Mercado-Ruiz, Jorge Nemesio; Mendoza-Wilson, Ana María
Food Reviews International, Vol. 31, Issue 3
DOI: 10.1080/87559129.2015.1015137

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi
journal, September 2018

Aguilar-Pontes, M. V.; Brandl, J.; McDonnell, E.
Studies in Mycology, Vol. 91
DOI: 10.1016/j.simyco.2018.10.001

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments
journal, February 2017

Daly, Paul; van Munster, Jolanda M.; Blythe, Martin J.
Biotechnology for Biofuels, Vol. 10, Issue 1
DOI: 10.1186/s13068-017-0700-9

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
journal, August 2008

Kim, Sangtae; Gupta, Nitin; Pevzner, Pavel A.
Journal of Proteome Research, Vol. 7, Issue 8
DOI: 10.1021/pr8001244

Redistribution of soil water by a saprotrophic fungus enhances carbon mineralization
journal, November 2015

Guhr, Alexander; Borken, Werner; Spohn, Marie
Proceedings of the National Academy of Sciences, Vol. 112, Issue 47
DOI: 10.1073/pnas.1514435112

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans
journal, March 2018

Khosravi, Claire; Battaglia, Evy; Kun, Roland S.
BMC Genomics, Vol. 19, Issue 1
DOI: 10.1186/s12864-018-4609-x

A New Black Aspergillus Species, A. vadensis, Is a Promising Host for Homologous and Heterologous Protein Production
journal, July 2004

de Vries, R. P.; Burgers, K.; van de Vondervoort, P. J. I.
Applied and Environmental Microbiology, Vol. 70, Issue 7
DOI: 10.1128/AEM.70.7.3954-3959.2004

MS-GF+ makes progress towards a universal database search tool for proteomics
journal, October 2014

Kim, Sangtae; Pevzner, Pavel A.
Nature Communications, Vol. 5, Issue 1
DOI: 10.1038/ncomms6277

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

Love, Michael I.; Huber, Wolfgang; Anders, Simon
Genome Biology, Vol. 15, Issue 12
DOI: 10.1186/s13059-014-0550-8

Regulators of plant biomass degradation in ascomycetous fungi
journal, June 2017

Benocci, Tiziano; Aguilar-Pontes, Maria Victoria; Zhou, Miaomiao
Biotechnology for Biofuels, Vol. 10, Issue 1
DOI: 10.1186/s13068-017-0841-x

2016 update of the PRIDE database and its related tools
journal, September 2016

Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi
Nucleic Acids Research, Vol. 44, Issue 22
DOI: 10.1093/nar/gkw880

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Title: Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Abstract

Citation Formats

MetaboAnalyst 3.0—making metabolomics more meaningful journal, April 2015

Woronin body-based sealing of septal pores journal, December 2017

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus journal, January 2013

DAnTE: a statistical tool for quantitative analysis of -omics data journal, May 2008

How does a hypha grow? The biophysics of pressurized growth in fungi journal, June 2011

A broader role for AmyR in Aspergillus niger: regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides journal, August 2011

Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae journal, January 2019

NCBI GEO: archive for functional genomics data sets—update journal, November 2012

Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin journal, September 2017

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood : Responses of journal, October 2018

The Structure and Function of the Vegetative Mycelium of Ectomycorrhizal Plants. i. Translocation of 14c-Labelled Carbon Between Plants Interconnected by a Common Mycelium journal, May 1986

A new self-assembled peroxisomal vesicle required for efficient resealing of the plasma membrane journal, March 2000

Physiological Significance of Network Organization in Fungi journal, September 2012

Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry journal, November 2006

FactoMineR : An R Package for Multivariate Analysis journal, January 2008

Biological solutions to transport network design journal, July 2007

Mycelial density profiles of fungi on heterogeneous media and their interpretation in terms of nutrient reallocation patterns journal, February 1995

Posttranscriptional Control of Gene Expression in Filamentous Fungi journal, March 1998

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13 C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS journal, October 2017

Genetic analysis and the construction of master strains for assignment of genes to six linkage groups in Aspergillus niger journal, November 1988

Switching from a Unicellular to Multicellular Organization in an Aspergillus niger Hypha journal, March 2015

Fungal enzyme sets for plant polysaccharide degradation journal, July 2011

Localization of growth and secretion of proteins in Aspergillus niger journal, August 1991

Analysis of fungal networks journal, April 2012

Aiming for the complete utilization of sugar-beet pulp: Examination of the effects of mild acid and hydrothermal pretreatment followed by enzymatic digestion journal, January 2011

A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics journal, August 2011

Simplified method for the measurement of total non-starch polysaccharides by gas-liquid chromatography of constituent sugars as alditol acetates journal, January 1984

Direct transfer of carbon between plants connected by vesicular–arbuscular mycorrhizal mycelium journal, January 1984

Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics journal, March 2009

Advances in proteomics data analysis and display using an accurate mass and time tag approach journal, January 2006

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization journal, August 2015

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger journal, November 2017

Isolation of Aspergillus niger creA mutants and effects of the mutations on expression of arabinases and L-arabinose catabolic enzymes journal, September 1997

HTSeq--a Python framework to work with high-throughput sequencing data journal, September 2014

Hyphal homing, fusion and mycelial interconnectedness journal, March 2004

The carbohydrate-active enzymes database (CAZy) in 2013 journal, November 2013

2016 update of the PRIDE database and its related tools journal, November 2015

Cytoplasmic Continuity Revisited: Closure of Septa of the Filamentous Fungus Schizophyllum commune in Response to Environmental Conditions journal, June 2009

Expression profiling of pectinolytic genes from Aspergillus niger journal, September 2002

Spatial Differentiation in the Vegetative Mycelium of Aspergillus niger journal, October 2007

Aspergillus Enzymes Involved in Degradation of Plant Cell Wall Polysaccharides journal, December 2001

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass journal, August 2015

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification journal, December 2016

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 journal, January 2007

Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon journal, April 2003

Wheat Bran Proteins: A Review of Their Uses and Potential journal, February 2015

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi journal, September 2018

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments journal, February 2017

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases journal, August 2008

Redistribution of soil water by a saprotrophic fungus enhances carbon mineralization journal, November 2015

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans journal, March 2018

A New Black Aspergillus Species, A. vadensis, Is a Promising Host for Homologous and Heterologous Protein Production journal, July 2004

MS-GF+ makes progress towards a universal database search tool for proteomics journal, October 2014

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal, December 2014

Regulators of plant biomass degradation in ascomycetous fungi journal, June 2017

2016 update of the PRIDE database and its related tools journal, September 2016

MetaboAnalyst 3.0—making metabolomics more meaningful
journal, April 2015

Woronin body-based sealing of septal pores
journal, December 2017

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus
journal, January 2013

DAnTE: a statistical tool for quantitative analysis of -omics data
journal, May 2008

How does a hypha grow? The biophysics of pressurized growth in fungi
journal, June 2011

A broader role for AmyR in Aspergillus niger: regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides
journal, August 2011

Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae
journal, January 2019

NCBI GEO: archive for functional genomics data sets—update
journal, November 2012

Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin
journal, September 2017

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood : Responses of
journal, October 2018

The Structure and Function of the Vegetative Mycelium of Ectomycorrhizal Plants. i. Translocation of 14c-Labelled Carbon Between Plants Interconnected by a Common Mycelium
journal, May 1986

A new self-assembled peroxisomal vesicle required for efficient resealing of the plasma membrane
journal, March 2000

Physiological Significance of Network Organization in Fungi
journal, September 2012

Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry
journal, November 2006

FactoMineR : An R Package for Multivariate Analysis
journal, January 2008

Biological solutions to transport network design
journal, July 2007

Mycelial density profiles of fungi on heterogeneous media and their interpretation in terms of nutrient reallocation patterns
journal, February 1995

Posttranscriptional Control of Gene Expression in Filamentous Fungi
journal, March 1998

Quantification of Lignin and Its Structural Features in Plant Biomass Using ¹³ C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS
journal, October 2017

Genetic analysis and the construction of master strains for assignment of genes to six linkage groups in Aspergillus niger
journal, November 1988

Switching from a Unicellular to Multicellular Organization in an Aspergillus niger Hypha
journal, March 2015

Fungal enzyme sets for plant polysaccharide degradation
journal, July 2011

Localization of growth and secretion of proteins in Aspergillus niger
journal, August 1991

Analysis of fungal networks
journal, April 2012

Aiming for the complete utilization of sugar-beet pulp: Examination of the effects of mild acid and hydrothermal pretreatment followed by enzymatic digestion
journal, January 2011

A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics
journal, August 2011

Simplified method for the measurement of total non-starch polysaccharides by gas-liquid chromatography of constituent sugars as alditol acetates
journal, January 1984

Direct transfer of carbon between plants connected by vesicular–arbuscular mycorrhizal mycelium
journal, January 1984

Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics
journal, March 2009

Advances in proteomics data analysis and display using an accurate mass and time tag approach
journal, January 2006

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization
journal, August 2015

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger
journal, November 2017

Isolation of Aspergillus niger creA mutants and effects of the mutations on expression of arabinases and L-arabinose catabolic enzymes
journal, September 1997

HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014

Hyphal homing, fusion and mycelial interconnectedness
journal, March 2004

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

2016 update of the PRIDE database and its related tools
journal, November 2015

Cytoplasmic Continuity Revisited: Closure of Septa of the Filamentous Fungus Schizophyllum commune in Response to Environmental Conditions
journal, June 2009

Expression profiling of pectinolytic genes from Aspergillus niger
journal, September 2002

Spatial Differentiation in the Vegetative Mycelium of Aspergillus niger
journal, October 2007

Aspergillus Enzymes Involved in Degradation of Plant Cell Wall Polysaccharides
journal, December 2001

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass
journal, August 2015

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification
journal, December 2016

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
journal, January 2007

Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon
journal, April 2003

Wheat Bran Proteins: A Review of Their Uses and Potential
journal, February 2015

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi
journal, September 2018

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments
journal, February 2017

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
journal, August 2008

Redistribution of soil water by a saprotrophic fungus enhances carbon mineralization
journal, November 2015

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans
journal, March 2018

A New Black Aspergillus Species, A. vadensis, Is a Promising Host for Homologous and Heterologous Protein Production
journal, July 2004

MS-GF+ makes progress towards a universal database search tool for proteomics
journal, October 2014

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

Regulators of plant biomass degradation in ascomycetous fungi
journal, June 2017

2016 update of the PRIDE database and its related tools
journal, September 2016