References
Abad, M., Ansuategui, M., & Bermejo, P. (2006). Active antifungal substances from natural sources. Archive for Organic Chemistry ,2007 (7), 116–145. doi:10.3998/ark.5550190.0008.711
Adams, A. S., Jordan, M. S., Adams, S. M., Suen, G., Goodwin, L. A., Davenport, K. W., Currie, C. R., & Raffa, K. F. (2011). Cellulose-degrading bacteria associated with the invasive woodwaspSirex noctilio . The ISME Journal , 5 (8), 1323–1331. doi: 10.1038/ismej.2011.14
Alves, M. J., Ferreira, I. C. F. R., Martins, A., & Pintado, M. (2012). Antimicrobial activity of wild mushroom extracts against clinical isolates resistant to different antibiotics. Journal of Applied Microbiology , 113 (2), 466–475. doi:10.1111/j.1365-2672.2012.05347.x
Arfi, Y., Levasseur, A., & Record, E. (2013). Differential gene expression in Pycnoporus coccineus during interspecific mycelial interactions with different competitors. Applied and Environmental Microbiology , 79 (21), 6626–6636. doi: 10.1128/AEM.02316-13
Bairoch, A., Boeckmann, B., Ferro, S., & Gasteiger, E. (2004). Swiss-Prot: juggling between evolution and stability. Briefings in bioinformatics , 5 (1): 39–55. doi: 10.1093/bib/5.1.39
Baldrian, P., Zrustová, P., Tláskal, V., Davidová, A., Merhautová, V., & Vrka, T. (2016). Fungi associated with decomposing deadwood in a natural beech-dominated forest. Fungal Ecology , 23 , 109–122. doi: 10.1016/j.funeco.2016.07.001
Blin, K., Medema, M. H., Kazempour, D., Fischbach, M. A., Breitling, R., Takano, E., & Weber, T. (2013). antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Research , 41 (W1), W204–W212. doi: 10.1093/nar/gkt449
Boddy, L. (2000). Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiology Ecology ,31 (3),185–194. doi:10.1016/S0168-6496(99)00093-8
Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., & Henrissat, B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Research , 37 , D233–D238. doi: 10.1093/nar/gkn663
Chen, L. F., Gong, Y. H., Cai, Y. L., Liu, W., Zhou, Y., Xiao, Y., … Bian, Y. B. (2016). Genome sequence of the edible cultivated mushroom Lentinula edodes (shiitake) reveals insights into lignocellulose degradation.PLoS ONE 11 (8), e0160336. doi: 10.1371/journal.pone.0160336
Coates, D., Rayner, A. D. M. (1985). Fungal population and community development in cut beech logs. III. Spatial dynamics, interactions and strategies. New Phytologist , 101 (1), 153–171. doi: 10.1111/j.1469-8137.1985.tb02823.x
Devi, S., Kiesewalter, H., Kovács, T. R., Frisvad, J. C., Weber, T., Larsen, T. O., … Ding, L. (2019). Depiction of secondary metabolites and antifungal activity of Bacillus velezensisDTU001. Synthetic and Systems Biotechnology , 4 (3), 142–149. doi: 10.1016/j.synbio.2019.08.002
de Wit, P. J. G. M., van der Burgt, A., Ökmen, B., Stergiopoulos, I., Abd-Elsalam, K. A., Aerts, A. L., … Cox, M. P. (2012). The genomes of the fungal plant pathogensCladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genetics , 8 (11), e1003088. doi: 10.1371/journal.pgen.1003088
[dataset] Eastwood, D. C., Floudas, D., Binder, M., Majcherczyk, A., Schneider, P., Aerts, A., … Watkinson, S. C. (2011). The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science , 333 (6043), 762–765. doi: 10.1126/science.1205411
Edman, M., & Eriksson, A. M. (2016). Competitive outcomes between wood-decaying fungi are altered in burnt wood. FEMS Microbiology Ecology , 92 (6), fiw068. doi: 10.1093/femsec/fiw068
Edman, M., & Fällström, I. (2013). An introduced tree species alters the assemblage structure and functional composition of wood-decaying fungi in microcosms. Forest Ecology and Management ,306 (15), 9–14. doi: 10.1016/j.foreco.2013.06.023
Eichlerová, I., Homolka, L., Žifčáková, L., Lisá, L., Dobiášová, P., & Baldrian, P. (2015). Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. Fungal Ecology , 13 , 10–22. doi: 10.1016/j.funeco.2014.08.002
Fernandes, A. F., Costa, L., Sousa, J. R., Zalocha, J., & Almeida, M. G. (2019). Biological activities of marine-derived actinomycetes: testing the aqueous extracellular phase of Streptomyces aculeolatus . Annals of Medicine , 51 (sup1), 44. doi: 10.1080/07853890.2018.1561899
Floudas, D., Bentzer, J., Ahrén, D., Johansson, T., & Tunlid, A. (2020). Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi. The ISME Journal , 14 (8), 1–14. doi: 10.1038/s41396-020-0667-6
[dataset] Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R. A., Henrissat, B., … Hibbett, D. S. (2012). The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science , 336 (6089), 1715–1719. doi: 10.1126/science.1221748
Friedemann, G., Leshem, Y., Kerem, L., Shacham, B., Bar-Massada, A., McClain, K. M., … Izhaki, I. (2016). Multidimensional differentiation in foraging resource use during breeding of two sympatric top predators. Scientific Reports , 6 , 35031. doi: 10.1038/srep35031
Fukami, T., Dickie, I. A., Wilkie, J. P., Paulus, B. C., Park, D., Roberts, A., … Allen, R. B. (2010). Assembly history dictates ecosystem functioning: evidence from wood decomposer communities.Ecology Letters , 13 (6), 675–684. doi: 10.1111/j.1461-0248.2010.01465.x
Fukasawa, Y., & Matuoka, S. (2015). Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan. Fungal Ecology , 18 , 75–82. doi: 10.1016/j.funeco.2015.09.008
García‐Palacios, P., McKie, B. G., Handa, I. T., Frainer, A., & Hättenschwiler, S. (2016). The importance of litter traits and decomposers for litter decomposition: a comparison of aquatic and terrestrial ecosystems within and across biomes. Functional Ecology , 30 (5), 819–829. doi: 10.1111/1365-2435.12589
Giweta, M. (2020). Role of litter production and its decomposition, and factors affecting the processes in a tropical forest ecosystem: a review. Journal of Ecology and Environment , 44 (1), 11. doi:10.1186/s41610-020-0151-2
Herzog, C., Hartmann, M., Frey, B., Stierli, B., & Brunner, I. (2019). Microbial succession on decomposing root litter in a drought-prone scots pine forest.The ISME Journal , 13 (2), 2346–2362. doi: 10.1038/s41396-019-0436-6
Holmer, L., Renvall, P., & Stenlid, J. (1997). Selective replacement between species of wood-rotting basidiomycetes, a laboratory study.Mycological Research , 101 (6), 714–720. doi: 10.1017/S0953756296003243
Huang, S. F., Chen, Z. L., Huang, G. R., Yu, T., Yang, P., Li, J., … Xu, A. L. (2012). HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Research , 22 (8), 1581–1588. doi: 10.1101/gr.133652.111.
Huang, S. F., Kang, M. J., & Xu, A. L. (2017). HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics , 33 , 2577–2579. doi: 10.1093/bioinformatics/btx220.
Johnston, S. R., Boddy, L., & Weightman, A. J. (2016). Bacteria in decomposing wood and their interactions with wood-decay fungi.FEMS Microbiology Ecology , 92 (11), fiw179. doi: 10.1093/femsec/fiw179
Jonkers, W., Rodriguez, E. A. E., Lee, K., Breakspear, A., May, G., Kistler, H. C. (2012). Metabolome and transcriptome of the interaction between Ustilago maydis and Fusarium verticillioides in vitro. Applied and Environmental Microbiology , 78 (10), 3656–3667. doi: 10.1128/AEM.07841-11
Katagiri, S., Shiba, T., Tohara, H., Yamaguchi, K., Hara, K., Nakagawa, K., … Iwata, T. (2019). Re-initiation of oral food intake following enteral nutrition alters oral and gut microbiota communities.Frontiers in Cellular and Infection Microbiology , 9 , 434. doi: 10.3389/fcimb.2019.00434
Keller, N. P., Turner, G., & Bennett, J. W. (2005). Fungal secondary metabolism – from biochemistry to genomics.Nature Reviews Microbiology , 3 (12), 937–947. doi: 10.1038/nrmicro1286
Kohler, A., Kuo, A., Nagy, L. G., Morin, E., Barry, K. W., Buscot, F., … Martin F. (2015). Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.Nature Genetics , 47 (4), 410–415. doi: 10.1038/ng.3223
Konno, K. (2011). Plant latex and other exudates as plant defense systems: roles of various defense chemicals and proteins contained therein. Phytochemistry , 72 (13), 1510–1530. doi: 10.1016/j.phytochem.2011.02.016
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research , 27 (5), 722–736. doi: 10.1101/gr.215087.116
Krah, F. S., Seibold, S., Brandl, R., Baldrian, P., Müller, J., & Bässler, C. (2018). Independent effects of host and environment on the diversity of wood-inhabiting fungi. Journal of Ecology , 106 , 1428–1442. doi: 10.1111/1365-2745.12939
Lam, K. K., Labutti, K., Khalak, A., & Tse, D. (2015). FinisherSC: a repeat-aware tool for upgradingde novoassembly using long reads. Bioinformatics , 31 , 1–8. doi:10.1093/bioinformatics/btv280
Lima, G., Arru, S., De Curtis, F., & Arras, G. (1999). Influence of antagonist, host fruit and pathogen on the biological control of postharvest fungal diseases by yeasts. Journal of Industrial Microbiology and Biotechnology , 23 (3), 223–229. doi:10.1038/sj.jim.2900727
Li, T. C., Yu, L. Y., Song, B., Song, Y., Li, L., Lin, X., & Lin, S. J. (2020). Genome improvement and core gene set refinement ofFugacium kawagutii . Microorganisms , 8 (1), 102. doi: 10.3390/microorganisms8010102
Liu, Y. C., Jan, S., & Bertil, S. (2013). Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data.Bioinformatics , 29 (3), 308–315. doi: 10.1093/bioinformatics/bts690
Martin, F., Kohler, A., Murat, C., Veneault-Fourrey, C., & Hibbett, D. S. (2016). Unearthing the roots of ectomycorrhizal symbioses. Nature Reviews Microbiology , 14 , 760–773. doi: 10.1038/nrmicro.2016.149
[dataset] Martinez, D., Larrondo, L. F., Putnam, N., Gelpk,e M. D., Huang, K., Chapman, J., … Rokhsar D. (2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporiumstrain RP78. Nature Biotechnology , 22 , 695–700. doi: 10.1038/nbt967
Mayjonade, B., Gouzy, J., Donnadieu, C., Pouilly, N., Marande, W., Callot, C., … Muños, S. (2016). Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Biotechniques , 61 (4), 203–205. doi: 10.2144/000114460
Moor, H., Nordén, J., Penttil, R., Siitonen, J., & Snll, T. (2020). Long-term effects of colonization‐extinction dynamics of generalist versus specialist wood‐decaying fungi. Journal of Ecology ,109 (1), 491–503. doi: 10.1111/1365-2745.13526
Nagy, L. G., Riley, R., Tritt, A., Adam, C., Daum, C., Floudas, D., … Larsson, K. H. (2016). Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Molecular Biology and Evolution , 33 (4), 959–970. doi: 10.1093/molbev/msv337
Niego, A. G., Raspé, O., Thongklang, N., Charoensup, R., Lumyong, S., Stadler, M., & Hyde, K. D. (2021). Taxonomy, diversity and cultivation of the Oudemansielloid/Xeruloid taxaHymenopellis , Mucidula , Oudemansiella , andXerula with respect to their bioactivities: a review.Journal of Fungi , 7 (1), 51. doi: 10.3390/jof7010051
Niemela, T., Renvall, P., & Pentilla, R. (1995). Interactions of fungi at late stages of wood decomposition. Annales Botanici Fennici ,32 (3), 141–152.
Oghenekaro, A. O., Kovalchuk, A., Raffaello, T., Camarero, S., & Asiegbu, F. O. (2020). Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions. Scientific Reports , 10 (1), 5250. doi: 10.1038/s41598-020-62150-4
Park, Y. J., Jeong, Y. U., & Kong, W. S. (2018). Genome sequencing and carbohydrate-active enzyme (CAZyme) repertoire of the white rot fungusFlammulina elastica . International Journal of Molecular Sciences , 19 (8), 2379. doi: 10.3390/ijms19082379
[dataset] Ohm, R. A., Riley, R., Salamov, A., Min, B., Choi, I. G., Grigoriev, I. V. (2014). Genomics of wood-degrading fungi. Fungal Genetics and Biology , 72 , 82–90. doi: 10.1016/j.fgb.2014.05.001
[dataset] Olson, A., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., … Stenlid, J. (2012). Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytologist , 194 (4), 1001–1013. doi: 10.1111/j.1469-8137.2012.04128.x
Polo, C. C., Pereira, L., Mazzafera, P., Flores-Borges, D. N. A., & Meneau, F. (2020). Correlations between lignin content and structural robustness in plants revealed by x-ray ptychography. Scientific Reports , 10 (1), 6023. doi: 10.1038/s41598-020-63093-6
Qin, J., Horak, E., Popa, F., Rexer, K. H., & Yang, Z. L. (2018). Species diversity, distribution patterns, and substrate specificity ofStrobilurus . Mycologia , 110 (3), 584–604. doi: 10.1080/00275514.2018.1463064
Rajala, T., Peltoniemi, M., Hantula, J., Mäkipää, R., & Pennanen, T. (2011). RNA reveals a succession of active fungi during the decay of Norway spruce logs. Fungal Ecology , 4 (6), 437–448. doi: 10.1016/j.funeco.2011.05.005
Rajala, T., Peltoniemi, M., Pennanen, T., & Mäkipää, R. (2010). Relationship between wood-inhabiting fungi determined by molecular analysis (DGGE) and quality of decaying logs. Canadian Journal of Forest Research , 40 (12), 2384–2397. doi: 10.1139/X10-176
[dataset] Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., … Grigorieva I. V. (2014). Extensive sampling of basidiomycete genomes demonstrate inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proceedings of the National Academy of Science , 111 (27), 9923–9928. doi: 10.1073/pnas.1400592111
Saha, P., & Roy-Barman, S. (2018). The role of the global regulator of secondary metabolism laea in different fungi. Current Journal of Applied Science and Technology , 31 (1), 1–5. doi: 10.9734/CJAST/2018/45867
Sasha, V., & Bhatnagar, J. M. (2019). An evolutionary signal to fungal succession during plant litter decay. FEMS Microbiology Ecology ,95 (10), fiz145. doi: 10.1093/femsec/fiz145
Sipos, G., Prasanna, A. N., Walter, M. C., O’Connor, E., Bálint, B., Krizsán, K., … Nagy L. G. (2017). Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungiArmillaria . Nature Ecology and Evolution , 1 (12), 1931–1941. doi: 10.1038/s41559-017-0347-8
Šnajdr, J., Cajthaml, T., Valášková, V., Merhautová, V., Petránková, M., Spetz, P., … Baldrian, P. (2011). Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition. FEMS Microbiology Ecology , 75 (2), 291–303. doi: 10.1111/j.1574-6941.2010.00999.x
Song, Z. W., Vail, A., Sadowsky, M. J., & Schilling, J. S. (2012). Competition between two wood-degrading fungi with distinct influences on residues. FEMS Microbiology Ecology , 79 (1), 109–117. doi: 10.1111/j.1574-6941.2011.01201.x
Stokland, J. N., Siitonen, J., & Jonsson, B. G. (2012). Biodiversity in Dead Wood. Cambridge, UK: Cambridge University Press.
[dataset] Suzuki, H., MacDonald, J., Syed, K., Salamov, A., Hori, C., Aerts, A., … Master, E. R. (2012). Comparative genomics of the white-rot fungi,Phanerochaete carnosa and P. chrysosporium , to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics , 13 , 444. doi: 10.1186/1471-2164-13-444
Varga, T., Krizsán, K., Földi, C., Dima, B., Sánchez-García, M., Sánchez-Ramírez, … Nagy L. G. (2019). Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecology and Evolution , 3 (4), 668–678. doi: 10.1038/s41559-019-0834-1
Voříšková, J., & Baldrian, P. (2013). Fungal community on decomposing leaf litter undergoes rapid successional changes. The ISME Journal , 7 (3), 477–486. doi: 10.1038/ismej.2012.116
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., … Earl, A. M. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE , 9 (11), e112963. doi: 10.1371/journal.pone.0112963
Wang, P. M., & Yang, Z. L. (2019). Two new taxa of theAuriscalpium vulgare species complex with substrate preferences.Mycological Progress , 18 (5), 641–652. doi: 10.1007/s11557-019-01477-3
Weng, C. H., Peng, X. W., & Han, Y. J. (2021). Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis. Biotechnology for Biofuels , 14 , 84. doi: 10.1186/s13068-021-01934-w
Wilson, C. L., Wisniewski, M. E., Biles, C. L., McLaughlin, R., Chalutz, E., & Droby, S. (1991). Biological control of post-harvest diseases of fruits and vegetables: alternatives to synthetic fungicides. Crop Protection , 10 (3), 172–177. doi: 10.1016/0261-2194(91)90039-T
Zhang, L. Y., & Wei, Y. L. (2016). Species diversity and distribution characters of wood-decaying fungi in Fenglin Nature Reverse. Chinese Journal of Ecology , 35 (10), 2745–2751. doi: 10.17520/biods.2018156
Zhao, H. X., Yan, B., Mo, S. M., Nie, S. Q., Li, Q. W., Ou, Q., … Jiang, C. J. (2019). Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis. Journal of Microbiology , 57 , 575–586. doi: 10.1007/s12275-019-8679-5
Zhao, Z., Liu, H., Wang, C., & Xu, J. R. (2013). Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics , 14 (1), 274. doi: 10.1186/1471-2164-14-274
Zhu, N., Huang, W., Wu, D., Chen, K., & He, Y. (2017). Quantitative visualization of pectin distribution maps of peach fruits.Scientific Reports , 7 (1), 9275. doi: 10.1038/s41598-017-09817-7