Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.

Laboratory of Environmental Microbiology Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 14220 Praha 4 Czech Republic

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Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.

Arneodo, J.D., Bressan, A., Lherminier, J., Michel, J., and Boudon-Padieu, E. (2008) Ultrastructural detection of an unusual intranuclear bacterium in Pentastiridius leporinus (Hemiptera: Cixiidae). J Invertebr Pathol 97: 310-313.

Bai, Y., Eijsink, V.G.H., Kielak, A.M., van Veen, J.A., and de Boer, W. (2016) Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 18: 38-49.

Baldrian, P. (2009) Microbial enzyme-catalyzed processes in soils and their analysis. Plant, Soil Environ 55: 370-378.

Baldrian, P., and Větrovský, T. (2012) Scaling down the analysis of environmental processes: monitoring enzyme activity in natural substrates on a millimeter resolution scale. Appl Environ Microbiol 78: 3473-3475.

Baldrian, P., Větrovský, T., Cajthaml, T., Dobiášová, P., Petránková, M., Šnajdr, J., and Eichlerová, I. (2013) Estimation of fungal biomass in forest litter and soil. Fungal Ecol 6: 1-11.

Beier, S., and Bertilsson, S. (2013) Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol 4: 149.

Berlemont, R., and Martiny, A.C. (2015) Genomic potential for polysaccharide deconstruction in bacteria. Appl Environ Microbiol 81: 1513-1519.

Berlemont, R., and Martiny, A.C. (2016) Glycoside hydrolases across environmental microbial communities. PLoS Comput Biol 12: e1005300.

Bissaro, B., Isaksen, I., Vaaje-Kolstad, G., Eijsink, V.G.H., and Røhr, Å.K. (2018) How a lytic polysaccharide monooxygenase binds crystalline chitin. Biochemistry 57: 1893-1906.

Bostrom, B., Comstedt, D., and Ekblad, A. (2007) Isotope fractionation and C-13 enrichment in soil profiles during the decomposition of soil organic matter. Oecologia 153: 89-98.

Bowman, S.M., and Free, S.J. (2006) The structure and synthesis of the fungal cell wall. Bioessays 28: 799-808.

Brabcová, V., Nováková, M., Davidová, A., and Baldrian, P. (2016) Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community. New Phytol 210: 1369-1381.

Brabcová, V., Štursová, M., and Baldrian, P. (2018) Nutrient content affects the turnover of fungal biomass in forest topsoil and the composition of associated microbial communities. Soil Biol Biochem 118: 187-198.

Brigham, C. (2018) Biopolymers. In Green Chemistry, Boston, MA: Elsevier, pp. 753-770.

Brounéus, K. (2008) Reconciliation and development. In Building a Future on Peace and Justice. Berlin, Heidelberg: Springer, pp. 203-216.

Cox, J., Hein, M.Y., Luber, C.A., Paron, I., Nagaraj, N., and Mann, M. (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13: 2513-2526.

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.

Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.

Eichorst, S.A., and Kuske, C.R. (2012) Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Appl Environ Microbiol 78: 2316-2327.

Ekblad, A., Wallander, H., Godbold, D.L., Cruz, C., Johnson, D., Baldrian, P., et al. (2013) The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling. Plant and Soil 366: 1-27.

Folders, J., Algra, J., Roelofs, M.S., Van Loon, L.C., Tommassen, J., and Bitter, W. (2001) Characterization of Pseudomonas aeruginosa chitinase, a gradually secreted protein. J Bacteriol 183: 7044-7052.

Gooday, G.W. (1990) Physiology of microbial degradation of chitin and chitosan. Biodegradation 1: 177-190.

Hagenbo, A., Clemmensen, K.E., Finlay, R.D., Kyaschenko, J., Lindahl, B.D., Fransson, P., and Ekblad, A. (2017) Changes in turnover rather than production regulate biomass of ectomycorrhizal fungal mycelium across a Pinus sylvestris chronosequence. New Phytol 214: 424-431.

Hammond, J.B.W., and Nichols, R. (1975) Changes in respiration and soluble carbohydrates during the post-harvest storage of mushrooms (Agaricus bisporus). J Sci Food Agric 26: 835-842.

Hendricks, J.J., Mitchell, R.J., Kuehn, K.A., and Pecot, S.D. (2016) Ectomycorrhizal fungal mycelia turnover in a longleaf pine forest. New Phytol 209: 1693-1704.

Himmel, M.E., Xu, Q., Luo, Y., Ding, S.-Y., Lamed, R., and Bayer, E.A. (2010) Microbial enzyme systems for biomass conversion: emerging paradigms. Biofuels 1: 323-341.

Huang, L., Zhang, H., Wu, P., Entwistle, S., Li, X., Yohe, T., et al. (2018) dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Res 46: D516-D521.

Hudler, G.W. (2000) Magical Mushrooms, Mischievous Molds, 7th ed. Princeton, NJ: Princeton University Press.

Lacombe-Harvey, M.È., Brzezinski, R., and Beaulieu, C. (2018) Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution. Appl Microbiol Biotechnol 102: 7219-7230.

Lee, H.S., Lee, H.J., Choi, S.W., Her, S., and Oh, D.H. (1997) Purification and characterization of antifungal chitinase from Pseudomonas sp. YHS-A2. J Microbiol Biotechnol 7: 107-113.

Lee, J., Jung, Y.-J., Lee, H.K., Hong, S.G., and Kim, O.-S. (2016) Complete genome sequence of Pedobacter cryoconitis PAMC 27485, a CRISPR-Cas system-containing psychrophile isolated from Antarctica. J Biotechnol 226: 74-75.

Lladó, S., López-Mondéjar, R., and Baldrian, P. (2017) Forest soil bacteria: diversity, involvement in ecosystem processes, and response to global change. Microbiol Mol Biol Rev 81: e00063-16.

Lladó, S., Žifčáková, L., Větrovský, T., Eichlerová, I., and Baldrian, P. (2016) Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition. Biol Fertil Soils 52: 251-260.

Lo, Y.-C., Chien, S.-C., Mishchuk, D.O., Slupsky, C.M., and Mau, J.-L. (2016) Quantification of water-soluble metabolites in medicinal mushrooms using proton NMR spectroscopy. Int J Med Mushrooms 18: 413-424.

Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M., and Henrissat, B. (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42: D490-D495.

López-Mondéjar, R., Brabcová, V., Štursová, M., Davidová, A., Jansa, J., Cajthaml, T., and Baldrian, P. (2018) Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling. ISME J 12: 1768-1778.

López-Mondéjar, R., Zühlke, D., Becher, D., Riedel, K., and Baldrian, P. (2016a) Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 6: 25279.

López-Mondéjar, R., Zühlke, D., Větrovský, T., Becher, D., Riedel, K., and Baldrian, P. (2016b) Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199. Biotechnol Biofuels 9: 104.

Majdi, H., Truus, L., Johansson, U., Nylund, J.E., and Wallander, H. (2008) Effects of slash retention and wood ash addition on fine root biomass and production and fungal mycelium in a Norway spruce stand in SW Sweden. For Ecol Manage 255: 2109-2117.

Margesin, R., Spröer, C., Schumann, P., and Schinner, F. (2003) Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 53: 1291-1296.

Meier, K.K., Jones, S.M., Kaper, T., Hansson, H., Koetsier, M.J., Karkehabadi, S., et al. (2018) Oxygen activation by Cu LPMOs in recalcitrant carbohydrate polysaccharide conversion to monomer sugars. Chem Rev 118: 2593-2635.

Melo-Nascimento, A.O.d.S., Treumann, C., Neves, C., Andrade, E., Andrade, A.C., Edwards, R., et al. (2018) Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater. Arch Microbiol 200: 1267-1278.

Mendoza, C.G., Cabo, A.P., Calonje, M., Galán, B., and Novaes-Ledieu, M. (1996) Chemical and structural differences in cell wall polysaccharides of two monokaryotic strains and their resulting dikaryon of Agaricus bisporus. Curr Microbiol 33: 211-215.

Nguyen, S.T.C., Freund, H.L., Kasanjian, J., and Berlemont, R. (2018) Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol 102: 1629-1637.

Novaes-Ledieu, M., and Mendoza, C.G. (1981) The cell walls of Agaricus bisporus and Agaricus campestris fruiting body hyphae. Can J Microbiol 27: 779-787.

Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., et al. (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42: D206-D214.

Psylinakis, E., Boneca, I.G., Mavromatis, K., Deli, A., Hayhurst, E., Foster, S.J., et al. (2005) Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracis. J Biol Chem 280: 30856-30863.

Reddy, V.S., and Saier, M.H. (2012) BioV Suite - a collection of programs for the study of transport protein evolution. FEBS J 279: 2036-2046.

Reyes, J.E., Venturini, M.E., Oria, R., and Blanco, D. (2004) Prevalence of Ewingella americana in retail fresh cultivated mushrooms (Agaricus bisporus, Lentinula edodes and Pleurotus ostreatus) in Zaragoza (Spain). FEMS Microbiol Ecol 47: 291-296.

Rodriguez-R, L.M., Gunturu, S., Harvey, W.T., Rosselló-Mora, R., Tiedje, J.M., Cole, J.R., and Konstantinidis, K.T. (2018) The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 46: W282-W288.

Roy Chowdhury, P., Pay, J., and Braithwaite, M. (2007) Isolation, identification and ecology of Ewingella americana (the causal agent of internal stipe necrosis) from cultivated mushrooms in New Zealand. Aust Plant Pathol 36: 424.

Saier, M.H. (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res 34: D181-D186.

Saito, A., Shinya, T., Miyamoto, K., Yokoyama, T., Kaku, H., Minami, E., et al. (2007) The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N,N′-diacetylchitobiose in Streptomyces coelicolor A3(2). Appl Environ Microbiol 73: 3000-3008.

Satola, B., Wübbeler, J.H., and Steinbüchel, A. (2013) Metabolic characteristics of the species Variovorax paradoxus. Appl Microbiol Biotechnol 97: 541-560.

Song, Y.S., Seo, D.J., and Jung, W.J. (2017) Identification, purification, and expression patterns of chitinase from psychrotolerant Pedobacter sp. PR-M6 and antifungal activity in vitro. Microb Pathog 107: 62-68.

Štáfková, J., Rada, P., Meloni, D., Žárský, V., Smutná, T., Zimmann, N., et al. (2018) Dynamic secretome of Trichomonas vaginalis: case study of β-amylases. Mol Cell Proteomics 17: 304-320.

Štursová, M., Žifčáková, L., Leigh, M.B., Burgess, R., Baldrian, P., Zifčáková, L., et al. (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80: 735-746.

Sun, X., Li, Y., Tian, Z., Qian, Y., Zhang, H., and Wang, L. (2019) A novel thermostable chitinolytic machinery of Streptomyces sp. F-3 consisting of chitinases with different action modes. Biotechnol Biofuels 12: 136.

Talamantes, D., Biabini, N., Dang, H., Abdoun, K., and Berlemont, R. (2016) Natural diversity of cellulases, xylanases, and chitinases in bacteria. Biotechnol Biofuels 9: 133-140.

Valášková, V., and Baldrian, P. (2006) Degradation of cellulose and hemicelluloses by the brown rot fungus Piptoporus betulinus - production of extracellular enzymes and characterization of the major cellulases. Microbiology 152: 3613-3622.

Van Dyk, J.S., and Pletschke, B.I. (2012) A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes-Factors affecting enzymes, conversion and synergy. Biotechnol Adv 30: 1458-1480.

Větrovský, T., and Baldrian, P. (2013) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 8: e57923.

Větrovský, T., Baldrian, P., and Morais, D. (2018) SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics 34: 2292-2294.

Větrovský, T., Voříšková, J., Šnajdr, J., Gabriel, J., and Baldrian, P. (2011) Ecology of coarse wood decomposition by the saprotrophic fungus Fomes fomentarius. Biodegradation 22: 709-718.

Viens, P., Dubeau, M.-P., Kimura, A., Desaki, Y., Shinya, T., Shibuya, N., et al. (2015) Uptake of chitosan-derived D-glucosamine oligosaccharides in Streptomyces coelicolor A3(2). FEMS Microbiol Lett 362: fnv048.

Wallander, H., Goransson, H., and Rosengren, U. (2004) Production, standing biomass and natural abundance of N-15 and C-13 in ectomycorrhizal mycelia collected at different soil depths in two forest types. Oecologia 139: 89-97.

Webster, J., & Weber, R. (2007). Introduction. Introduction to Fungi, (1-39). New York, NY: Cambridge University Press. https://doi.org/10.1017/CBO9780511809026.

Wickham, H. (2009) ggplot2. New York, NY: Springer.

Wieczorek, A.S., Schmidt, O., Chatzinotas, A., von Bergen, M., Gorissen, A., and Kolb, S. (2019) Ecological functions of agricultural soil bacteria and microeukaryotes in chitin degradation: a case study. Front Microbiol 10: 1293.

Wilmotte, A., Van der Auwera, G., and De Wachter, R. (1993) Structure of the 16 S ribosomal RNA of the thermophilic cyanobacterium chlorogloeopsis HTF (‘Mastigocladus laminosus HTF’) strain PCC7518, and phylogenetic analysis. FEBS Lett 317: 96-100.

Xiao, X., Wang, F., Saito, A., Majka, J., Schlosser, A., and Schrempf, H. (2002) The novel Streptomyces olivaceoviridis ABC transporter Ngc mediates uptake of N-acetylglucosamine and N, N′-diacetylchitobiose. Mol Genet Genomics 267: 429-439.

Yang, J.-K., Zhang, J.-J., Yu, H.-Y., Cheng, J.-W., and Miao, L.-H. (2014) Community composition and cellulase activity of cellulolytic bacteria from forest soils planted with broad-leaved deciduous and evergreen trees. Appl Microbiol Biotechnol 98: 1449-1458.

Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67: 1613-1617.

Žifčáková, L., Větrovský, T., Lombard, V., Henrissat, B., Howe, A., and Baldrian, P. (2017) Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome 5: 122.

Zimmerman, A.E., Martiny, A.C., and Allison, S.D. (2013) Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J 7: 1187-1199.

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