Tuber pseudohimalayense ascomata-compartments strongly select their associated bacterial microbiome from nearby pine forest soils independently of their maturation stage

Pedobiologia - Tập 87 - Trang 150743 - 2021
Dong Liu1, Caspar C.C. Chater2, Fuqiang Yu1, Jesús Perez-Moreno3
1The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
2Department of Natural Capital and Plant Health, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
3Colegio de Postgraduados, Campus Montecillo, Microbiología, Edafología, Texcoco, 56230, Mexico

Tài liệu tham khảo

Antony-Babu, 2013, An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards, J. Appl. Microbiol., 115, 163, 10.1111/jam.12205 Antony-Babu, 2014, Black truffle - associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles, Environ. Microbiol., 16, 2831, 10.1111/1462-2920.12294 Atkinson, 2000, The beneficial rhizosphere: a dynamic entity, Appl. Soil Ecol., 15, 99, 10.1016/S0929-1393(00)00084-6 Baragatti, 2019, Influence of annual climatic variations, climate changes, and sociological factors on the production of the Périgord black truffle (Tuber melanosporum Vittad.) from 1903–1904 to 1988–1989 in the Vaucluse (France), Mycorrhiza, 29, 113, 10.1007/s00572-018-0877-1 Barbieri, 2005, New evidence for bacterial diversity in the ascoma of the ectomycorrhizal fungus Tuber borchii Vittad, FEMS Microbiol. Lett., 247, 23, 10.1016/j.femsle.2005.04.027 Barbieri, 2010, New evidence for nitrogen fixation within the Italian white truffle Tuber magnatum, Fungal Biol., 114, 936, 10.1016/j.funbio.2010.09.001 Barbieri, 2016, Truffle-associated bacteria: extrapolation from diversity to function, 301 Benucci, 2016, The truffle microbiome: species and geography effects on bacteria associated with fruiting bodies of hypogeous pezizales, Microb. Ecol., 72, 4, 10.1007/s00248-016-0755-3 Benucci, 2012, 265 Büntgen, 2017, New insights into the complex relationship between weight and maturity of Burgundy truffles (Tuber aestivum), PLoS One, 12, 10.1371/journal.pone.0170375 Caboni, 2020, Multi-platform metabolomic approach to discriminate ripening markers of black truffles (Tuber melanosporum), Food Chem., 319, 10.1016/j.foodchem.2020.126573 Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Chen, 2011, Delimitation of Tuber pseudohimalayense and T. pseudoexcavatum based on morphological and molecular data, Cryptogam. Mycol., 32, 83, 10.7872/crym.v32.iss1.2012.083 Chen, 2019, Chinese black truffle-associated bacterial communities of Tuber indicum from different geographical regions with Nitrogen fixing bioactivity, Front. Microbiol., 10, 2515, 10.3389/fmicb.2019.02515 Cheng, 2013, 5’-Serial analysis of gene expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea, BMC Genomics, 14, 195, 10.1186/1471-2164-14-195 De Miguel, 2014, Ectomycorrhizal fungus diversity and community structure with natural and cultivated truffle hosts: applying lessons learned to future truffle culture, Mycorrhiza, 24, 5, 10.1007/s00572-013-0554-3 Deveau, 2016, Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development, Mycorrhiza, 26, 389, 10.1007/s00572-015-0679-7 Dixon, 2003, VEGAN, a package of R functions for community ecology, J. Veg. Sci., 14, 927, 10.1111/j.1654-1103.2003.tb02228.x Fierer, 2007, Toward an ecological classification of soil bacteria, Ecology, 88, 1354, 10.1890/05-1839 Frank, 2005, On the nutritional dependence of certain trees on root symbiosis with belowground fungi (an English translation of A.B. Frank’s classic paper of 1885), Mycorrhiza, 15, 267, 10.1007/s00572-004-0329-y Halsey, 2016, Bacterial selection by mycospheres of Atlantic rainforest mushrooms, Antonie Van Leeuwenhoek, 109, 1353, 10.1007/s10482-016-0734-1 Harki, 2006, Maturation-associated alterations of the biochemical characteristics of the black truffle Tuber melanosporum Vitt, Food Chem., 99, 394, 10.1016/j.foodchem.2005.08.030 Jayasinghearachchi, 2004, Can mushrooms fix atmospheric nitrogen?, J. Biosci., 29, 293, 10.1007/BF02702611 Langille, 2013, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 31, 814, 10.1038/nbt.2676 Le Tacon, 2013, Carbon transfer from the host to Tuber melanosporum mycorrhizas and ascocarps followed using a 13C pulse-labeling technique, PLoS One, 8, 10.1371/journal.pone.0064626 Le Tacon, 2014, Climatic variations explain annual fluctuations in French Périgord black truffle wholesale markets but do not explain the decrease in black truffle production over the last 48 years, Mycorrhiza, 24, 115, 10.1007/s00572-014-0568-5 Le Tacon, 2016, Certainties and uncertainties about the life cycle of the Périgord black truffle (Tuber melanosporum Vittad.), Ann. For. Sci., 73, 105, 10.1007/s13595-015-0461-1 Li, 2018, Chinese Black Truffle (Tuber indicum) alters the ectomycorrhizosphere and endoectomycosphere microbiome and metabolic profiles of the host tree Quercus aliena, Front. Microbiol., 9 Liu, 2016, Is there a convergence of deciduous leaf litter stoichiometry, biochemistry and microbial population during decay?, Geoderma, 272, 93, 10.1016/j.geoderma.2016.03.005 Liu, 2017, Microbial functionality as affected by experimental warming of a temperate mountain forest soil—a metaproteomics survey, Appl. Soil Ecol., 117–118, 196, 10.1016/j.apsoil.2017.04.021 Liu, 2019, Geographic distance and soil microbial biomass carbon drive biogeographical distribution of fungal communities in Chinese Loess Plateau soils, Sci. Total Environ., 660, 1058, 10.1016/j.scitotenv.2019.01.097 Lozupone, 2011, UniFrac: an effective distance metric for microbial community comparison, ISME J., 10.1038/ismej.2010.133 Magoč, 2011, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, 27, 2957, 10.1093/bioinformatics/btr507 Mandrile, 2020, Near-infrared spectroscopy as a new method for post-harvest monitoring of white truffles, Mycol. Prog., 19, 329, 10.1007/s11557-020-01561-z McMurdie, 2014, Waste not, want not: why rarefying microbiome data is inadmissible, PLoS Comput. Biol., 10, 10.1371/journal.pcbi.1003531 Moreno, 1997, Tuber pseudohimalayensesp. nov. an asiatic species commercialized in Spain, similar to the “perigord” truffle, Mycotaxon, 63, 217 Nelson, 2007, Microbial environmental genomics, Microb. Ecol., 53, 367, 10.1007/s00248-007-9214-5 Oh, 2016, Distinctive feature of microbial communities and bacterial functional profiles in Tricholoma matsutake dominant soil, PLoS One, 11, 10.1371/journal.pone.0168573 Pacioni, 2007, Isolation and characterization of some mycelia inhabiting Tuber ascomata, Mycol. Res., 111, 1450, 10.1016/j.mycres.2007.08.016 Pacioni, 2014, Instrumental monitoring of the birth and development of truffles in a Tuber melanosporum orchard, Mycorrhiza, 10.1007/s00572-014-0561-z Pavić, 2013, Actinobacteria may influence white truffle (Tuber magnatum Pico) nutrition, ascocarp degradation and interactions with other soil fungi, Fungal Ecol., 6, 527, 10.1016/j.funeco.2013.05.006 Perlińska-Lenart, 2020, Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.), Archiv. Microbiol., 202, 2727, 10.1007/s00203-020-02002-x Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res. Ramette, 2007, Multivariate analyses in microbial ecology, FEMS Microbiol. Ecol., 62, 142, 10.1111/j.1574-6941.2007.00375.x Salerni, 2014, Ectomycorrhizal communities above and below ground and truffle productivity in a Tuber aestivum orchard, For. Syst., 23, 329 Sánchez-Osuna, 2017, Comparative genomics of the DNA damage-inducible network in the Patescibacteria, Environ. Microbiol., 19, 3465, 10.1111/1462-2920.13826 Sbrana, 2002, Diversity of culturable bacterial populations associated to Tuber borchii ectomycorrhizas and their activity on T. borchii mycelial growth, FEMS Microbiol. Lett., 211, 195, 10.1111/j.1574-6968.2002.tb11224.x Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 10.1128/AEM.01541-09 Segata, 2011, Metagenomic biomarker discovery and explanation, Genome Biol., 12, R60, 10.1186/gb-2011-12-6-r60 Shah, 2020, An investigation on changes in composition and antioxidant potential of mature and immature summer truffle (Tuber aestivum), Eur. Food Res. Technol., 246, 723, 10.1007/s00217-020-03438-7 Vahdatzadeh, 2015, The role of the microbiome of truffles in aroma formation: a meta-analysis approach, Appl. Environ. Microbiol., 81, 6946, 10.1128/AEM.01098-15 VanInsberghe, 2015, Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils, ISME J., 9, 2435, 10.1038/ismej.2015.54 Wang, 1998, Tuber pseudoexcavatumsp. nov. A new species from China commercialised in Spain, France and Italy with additional comments on Chinese truffles, Cryptogam., Mycol., 19, 113 Wang, 2012, Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa, Fungal Genet. Biol., 49, 405, 10.1016/j.fgb.2012.03.004 Wang, 2014, Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa, Eukaryot. Cell, 13, 154, 10.1128/EC.00248-13 Wiese, 2008, A new member of the family Micromonosporaceae, Planosporangium flavigriseumgen. nov., sp. nov, Int. J. Syst. Evol. Microbiol., 58, 1324, 10.1099/ijs.0.65211-0 Xiong, 2016, Comparison of fungal community in black pepper-vanilla and vanilla monoculture systems associated with vanilla fusarium wilt disease, Front. Microbiol., 7, 117, 10.3389/fmicb.2016.00117 Xue, 2008, Soil microbial community structure in diverse land use systems: a comparative study using Biolog, DGGE, and PLFA Analyses, Pedosphere, 18, 653, 10.1016/S1002-0160(08)60060-0 Zarivi, 2015, Validation of reference genes for quantitative real-time PCR in Périgord black truffle (Tuber melanosporum) developmental stages, Phytochemistry, 116, 78, 10.1016/j.phytochem.2015.02.024 Zeppa, 2004, Determination of specific volatile organic compounds synthesised during Tuber borchii fruit body development by solid-phase microextraction and gas chromatography mass spectrometry, Rapid Commun. Mass Spectrom., 18, 199, 10.1002/rcm.1313 Zhao, 2019, Intra-horizon differentiation of the bacterial community and its co-occurrence network in a typical Plinthic horizon, Sci. Total Environ., 678, 692, 10.1016/j.scitotenv.2019.04.305 Zhu, 2018, Major genes expression of storage carbohydrate metabolism in fruiting body formation of Pholiota microspora, Plant Gene, 14, 83, 10.1016/j.plgene.2018.05.003