Fungi and bacteria in the rhizosphere of Cryptomeria japonica exhibited different community assembly patterns at regional scales in East Asia

Rhizosphere - Tập 28 - Trang 100807 - 2023
Keisuke Obase1, Yudai Kitagami2, Toko Tanikawa3, Chien-Fan Chen4, Yosuke Matsuda2
1Woodland Bioecoloy Group, Hokkaido Research Center, Forestry and Forest Products Research Institute, Japan
2Laboratory of Forest Mycology, Graduate School of Bioresources, Mie University, Japan
3Laboratory of Plant and Soil Systems, Department of Forest and Environmental Resources Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Japan
4Forest Ecology Division, Taiwan Forestry Research Institute, Taiwan

Tài liệu tham khảo

Abarenkov, 2010, The UNITE database for molecular identification of fungi—recent updates and future perspectives, New Phytol., 186, 281, 10.1111/j.1469-8137.2009.03160.x Abe, 2021, Soil bacterial community composition in Cryptomeria japonica plantation at different times after clear-cutting, Forests, 12, 754, 10.3390/f12060754 Ai, 2018, Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation, Geoderma, 319, 156, 10.1016/j.geoderma.2018.01.010 Alabid, 2019, Endofungal bacteria increase fitness of their host fungi and impact their association with crop plants, Curr. Issues Mol. Biol., 30, 59, 10.21775/cimb.030.059 Arbizu, 2017 Aslani, 2022, Towards revealing the global diversity and community assembly of soil eukaryotes, Ecol. Lett., 25, 65, 10.1111/ele.13904 Blois, 2014, A framework for evaluating the influence of climate, dispersal limitation, and biotic interactions using fossil pollen associations across the late Quaternary, Ecography, 37, 1095, 10.1111/ecog.00779 Bolyen, 2019, Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2, Nat. Biotechnol., 37, 852, 10.1038/s41587-019-0209-9 Brunel, 2020, Towards unraveling macroecological patterns in rhizosphere microbiomes, Trends Plant Sci., 25, 1017, 10.1016/j.tplants.2020.04.015 Chen, 2012, Associating microbiome composition with environmental covariates using generalized UniFrac distances, Bioinformatics, 28, 2106, 10.1093/bioinformatics/bts342 Dassen, 2017, Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity, Mol. Ecol., 26, 4085, 10.1111/mec.14175 de Boer, 2019, Pathogen suppression by microbial volatile organic compounds in soils, FEMS Microbiol. Ecol., 95 Deng, 2018, Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun, Environ. Pollut., 237, 1088, 10.1016/j.envpol.2017.11.037 Deng, 2017, Fungal endophytes and their interactions with plants in phytoremediation: a review, Chemosphere, 168, 1100, 10.1016/j.chemosphere.2016.10.097 Djotan, 2022, Amplicon sequencing reveals the arbuscular mycorrhizal fungal community composition in Cryptomeria japonica at one local site, J. For. Res., 27, 399, 10.1080/13416979.2022.2043516 Dormann, 2018, Biotic interactions in species distribution modelling: 10 questions to guide interpretation and avoid false conclusions, Glob. Ecol. Biogeogr., 27, 1004, 10.1111/geb.12759 Dray Faust, 2016, CoNet app: inference of biological association networks using Cytoscape, F1000Res., 5, 1519, 10.12688/f1000research.9050.1 Finzi, 2015, Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles, Glob. Change Biol., 21, 2082, 10.1111/gcb.12816 1976, Classification of forest soils in Japan (1975), Bull. Govern. For. Exp. Stn., 280, 1 Gao, 2022, Community of soil-inhabiting myxomycetes shares similar assembly mechanisms with fungi, and is affected by bacterial community in subtropical forests of China, Soil Biol. Biochem., 175, 10.1016/j.soilbio.2022.108854 Goberna, 2019, Incorporating phylogenetic metrics to microbial co-occurrence networks based on amplicon sequences to discern community assembly processes, Mol. Ecol. Resour., 19, 1552, 10.1111/1755-0998.13079 Goberna, 2022, Cautionary notes on the use of co-occurrence networks in soil ecology, Soil Biol. Biochem., 166, 10.1016/j.soilbio.2021.108534 Goslee, 2007, The ecodist package for dissimilarity-based analysis of ecological data, J. Stat. Softw., 22, 1, 10.18637/jss.v022.i07 Hart, 2002, Taxonomic basis for variation in the colonization strategy of arbuscular mycorrhizal fungi, New Phytol., 1532, 335, 10.1046/j.0028-646X.2001.00312.x He, 2018, Induced salt tolerance of perennial ryegrass by a novel bacterium strain from the rhizosphere of a desert shrub Haloxylon ammodendron, Int. J. Mol. Sci., 19, 469, 10.3390/ijms19020469 Herlemann, 2011, Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea, ISME J., 5, 1571, 10.1038/ismej.2011.41 Hishi, 2017, Changes in the anatomy, morphology and mycorrhizal infection of fine root systems of Cryptomeria japonica in relation to stand ageing, Tree Physiol., 37, 61 Karimi, 2018, Biogeography of soil bacteria and archaea across France, Sci. Adv., 4, 10.1126/sciadv.aat1808 Kielak, 2016, The ecology of Acidobacteria: moving beyond genes and genomes, Front. Microbiol., 7, 744, 10.3389/fmicb.2016.00744 Kira, 1948, On the altitudinal arrangement of climatic zones in Japan, Kanti-Nogaku., 2, 143 Kitagami, 2022, Effects of climatic and edaphic conditions on structuring patterns of soil nematode communities in Japanese cedar (Cryptomeria japonica) plantations, For. Ecol. Manag., 524, 10.1016/j.foreco.2022.120518 Kwak, 2018, Rhizosphere microbiome structure alters to enable wilt resistance in tomato, Nat. Biotech., 36, 1100, 10.1038/nbt.4232 Lauber, 2008, The influence of soil properties on the structure of bacterial and fungal communities across land-use types, Soil Biol. Biochem., 40, 2407, 10.1016/j.soilbio.2008.05.021 Li, 2020, Rare fungus, Mortierella capitata, promotes crop growth by stimulating primary metabolisms related genes and reshaping rhizosphere bacterial community, Soil Biol. Biochem., 151, 10.1016/j.soilbio.2020.108017 Lichstein, 2007, Multiple regression on distance matrices: a multivariate spatial analysis tool, Plant Ecol., 188, 117, 10.1007/s11258-006-9126-3 Liu, 2019, Deciphering microbiome related to rusty roots of Panax ginseng and evaluation of antagonists against pathogenic Ilyonectria, Front. Microbiol., 10, 1350, 10.3389/fmicb.2019.01350 Liu, 2019, Changes in rhizosphere bacterial and fungal community composition with vegetation restoration in planted forests, Land Degrad. Dev., 30, 1147, 10.1002/ldr.3275 Lladó, 2017, Forest soil bacteria: diversity, involvement in ecosystem processes, and response to global change, Microbiol. Mol. Biol. Rev., 81, 10.1128/MMBR.00063-16 Luan, 2020, Organism body size structures the soil microbial and nematode community assembly at a continental and global scale, Nat. Commun., 11, 6406, 10.1038/s41467-020-20271-4 Marschner, 2001, Soil and plant specific effects on bacterial community composition in the rhizosphere, Soil Biol. Biochem., 33, 1437, 10.1016/S0038-0717(01)00052-9 Matsuda, 2021, Colonization status and community structure of arbuscular mycorrhizal fungi in the coniferous tree, Cryptomeria japonica, with special reference to root orders, Plant Soil, 468, 423, 10.1007/s11104-021-05147-w McDonald, 2012, An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, ISME J., 6, 610, 10.1038/ismej.2011.139 Obase, 2019, Extending the hyphal area of the ectomycorrhizal fungus Laccaria parva co–cultured with ectomycorrhizosphere bacteria on nutrient agar plate, Mycoscience, 60, 95, 10.1016/j.myc.2018.12.002 Obase, 2020, Effects of bacterial strains isolated from the ectomycorrhizal roots of Laccaria parva on sporocarp production by the fungus in vitro, Mycoscience, 61, 9, 10.1016/j.myc.2019.10.002 Oksanen, 2020, 5 Ozimek, 2020, Mortierella species as the plant growth-promoting fungi present in the agricultural soils, Agriculture, 11, 7, 10.3390/agriculture11010007 Peay, 2017, Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation–climate gradient, FEMS Microbiol. Ecol., 93, fix045, 10.1093/femsec/fix045 Põlme, 2020, FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles, Fungal Divers., 105, 1, 10.1007/s13225-020-00466-2 2021, vol. 2021 Raklami, 2019, Use of rhizobacteria and mycorrhizae consortium in the open field as a strategy for improving crop nutrition, productivity and soil fertility, Front. Microbiol., 10, 1106, 10.3389/fmicb.2019.01106 Revelle, 2021 Rousk, 2010, Soil bacterial and fungal communities across a pH gradient in an arable soil, ISME J., 4, 1340, 10.1038/ismej.2010.58 Schmid, 2019, Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long-term biodiversity experiment, Mol. Ecol., 28, 863, 10.1111/mec.14987 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 Shen, 2017, Verrucomicrobial elevational distribution was strongly influenced by soil pH and carbon/nitrogen ratio, J. Soil Sediment, 17, 2449, 10.1007/s11368-017-1680-x Shi, 2020, Assembly of rhizosphere microbial communities in Artemisia annua: recruitment of plant growth-promoting microorganisms and inter-kingdom interactions between bacteria and fungi, Plant Soil, 470, 127, 10.1007/s11104-021-04829-9 Shigyo, 2022, Slope–induced factors shape bacterial communities in surface soils in a forested headwater catchment, Catena, 214, 10.1016/j.catena.2022.106253 2014 Stegen, 2013, Quantifying community assembly processes and identifying features that impose them, ISME J., 7, 2069, 10.1038/ismej.2013.93 Tanikawa, 2014, Acidification processes in soils with different acid buffering capacity in Cryptomeria japonica and Chamaecyparis obtusa forests over two decades, For. Ecol. Manag., 334, 284, 10.1016/j.foreco.2014.08.036 Tedersoo, 2014, Global diversity and geography of soil fungi, Science, 346, 10.1126/science.1256688 Toju, 2012, High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples, PLoS One, 7, 10.1371/journal.pone.0040863 Tripathi, 2018, Soil pH mediates the balance between stochastic and deterministic assembly of bacteria, ISME J., 12, 1072, 10.1038/s41396-018-0082-4 Tsumura, 2020, Effects of the last glacial period on genetic diversity and genetic differentiation in Cryptomeria japonica in East Asia, Tree Genet. Genomes, 16, 1, 10.1007/s11295-019-1411-0 van der Heul, 2018, Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era, Nat. Prod. Rep., 35, 575, 10.1039/C8NP00012C Wang, 2018, Precipitation drives the biogeographic distribution of soil fungal community in Inner Mongolian temperate grasslands, J. Soil Sediment., 18, 222, 10.1007/s11368-017-1727-z Xia, 2016, Biogeographic distribution patterns of bacteria in typical Chinese forest soils, Front. Microbiol., 7, 1106, 10.3389/fmicb.2016.01106 Xie, 2024, Converse (deterministic and stochastic) ecological process drive soil bacterial and fungal community assembly in subtropical forest, Appl. Soil Ecol., 193, 10.1016/j.apsoil.2023.105129 Zeng, 2019, Biogeography and the driving factors affecting forest soil bacteria in an arid area, Sci. Total Environ., 680, 124, 10.1016/j.scitotenv.2019.04.184 Zhang, 2018, Biogeography and ecological processes affecting root-associated bacterial communities in soybean fields across China, Sci. Total Environ., 627, 20, 10.1016/j.scitotenv.2018.01.230 Zhang, 2018, Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale, Soil Biol. Biochem., 118, 178, 10.1016/j.soilbio.2017.12.011 Zhao, 2019, Change in soil bacterial community during secondary succession depend on plant and soil characteristics, Catena, 173, 246, 10.1016/j.catena.2018.10.024 Zheng, 2020, Climatic factors have unexpectedly strong impacts on soil bacterial β-diversity in 12 forest ecosystems, Soil Biol. Biochem., 142, 10.1016/j.soilbio.2019.107699 Zou, 2021, Depression of the soil arbuscular mycorrhizal fungal community by the canopy gaps in a Japanese cedar (Cryptomeria japonica) plantation on Lushan Mountain, subtropical China, PeerJ, 9, 10.7717/peerj.10905